Currently, the most effective treatment is transferring the affected fish to a freshwater bath for a period of 2 to 3 hours. This is achieved by towing the sea cages into fresh water, or pumping the fish from the sea cage to a tarp filled with fresh water. Mortality rates have been lowered by adding Levamisole to the water until the saturation is above 10ppm. Due to the difficulty and expense of treatment, the productivity of salmon aquaculture is limited by access to a source of fresh water. Chloramine and chlorine dioxide have also been used. Other potential in-feed treatments such as immunosupportive-based feeds, mucolytic compounds such as L-cysteine ethyl ester and the parasticide bithionol have been tested with some success although not developed for commercial use.

Thousand cankers disease can be spread by moving infected black walnut wood. Trees intended for shipment should be inspected for dieback and cankers and galleries after harvest. G. morbidia or the walnut twig beetle ("Pityophthorus juglandis") are not currently known to be moved with walnut seed . There is currently no chemical therapy or prevention available for the disease making it difficult to control the spread of the disease from the west to the eastern united states. Wood from infected trees can still be used for commercial value, but safety measures such as removing the bark, phloem, and cambium to reduce the risk of spreading the disease with shipment. Quarantines have been put in place in some states to reduce the potential movement of fungus or beetle from that region. On May 17th, 2010, the Director of the Michigan Department of Agriculture issued a quarantine from affected states to protect Michigan’s black walnut ecology and production. Contacting the appropriate entities about possible infections is important to stopping or slowing the spread of thousand cankers disease.

Several antibiotics are available for the treatment of redmouth disease in fish. Vaccines can also be used in the treatment and prevention of disease. Management factors such as maintaining water quality and a low stocking density are essential for disease prevention.

The use of a seven-way clostridial vaccination is the most common, cheapest, and efficacious preventative measure taken against blackleg. Burning the upper layer of soil to eradicate left-over spores is the best way to stop the spread of blackleg from diseased cattle. Diseased cattle should be isolated. Treatment is generally unrewarding due to the rapid progression of the disease, but penicillin is the drug of choice for treatment. Treatment is only effective in the early stages and as a control measure.

Dr. Oliver Morris (O.M.) Franklin made a significant contribution to the welfare of cattle and the livestock industry with his development of the blackleg vaccine. Franklin developed the original method of giving the vaccine while at Kansas State Agriculture College using live cattle. Franklin and another graduate veterinarian founded the original Kansas Blackleg Serum Co. in Wichita in 1916.

Amoebic gill disease (AGD) is a potentially fatal disease of some marine fish. It is caused by "Neoparamoeba perurans", the most important amoeba in cultured fish. It primarily affects farm raised fish of the Salmonidae family, most notably affecting the Tasmanian Atlantic Salmon (Salmo salar) industry, costing the A$20 million a year in treatments and lost productivity. Turbot, bass, bream, sea urchins and crabs have also been infected.

The disease has also been reported affecting the commercial salmon fisheries of the United States, Australia, New Zealand, France, Spain, Ireland and Chile. It was first diagnosed in the summer of 1984/1985 in populations of Atlantic Salmon off the east coast of Tasmania and was found to be caused by the "Neoparamoeba perurans" n.sp.

Sodium chloride is believed to mitigate the reproduction of Velvet, however this treatment is not itself sufficient for the complete eradication of an outbreak. Additional, common medications added directly to the fish's environment include copper sulfate, methylene blue, formalin, malachite green and acriflavin, all of which can be found in common fish medications designed specifically to combat this disease. Additionally, because Velvet parasites derive a portion of their energy from photosynthesis, leaving a tank in total darkness for seven days provides a helpful supplement to chemical curatives. Finally, some enthusiasts recommend raising the water temperature of an infected fish's environment, in order to quicken the life cycle (and subsequent death) of Velvet parasites; however this tactic is not practical for all fish, and may induce immunocompromising stress.

With extra care taken to the health of the shrimp, it is possible to prevent cases of black gill disease. The water should have 10-20 parts per thousand parts salinity and filtered.

As "Flavobacterium columnare" is Gram-negative, fish can be treated with a combination of the antibiotics furan-2 and kanamycin administered together. A medicated fish bath (using methylene blue or potassium permanganate and salt), is generally a first step, as well lowering the aquarium temperature to 75 °F (24 °C) is a must, since columnaris is much more virulent at higher temperatures, especially 85–90 °F.

Medicated food containing oxytetracycline is also an effective treatment for internal infections, but resistance is emerging. Potassium permanganate, copper sulfate, and hydrogen peroxide can also be applied externally to adult fish and fry, but can be toxic at high concentrations. Vaccines can also be given in the face of an outbreak or to prevent disease occurrence.

Bacterial leaf streak of wheat is not easily prevented, but can be controlled with clean seed and resistance. Some foliar products, such as pesticides and antibiotic compounds, have been tested for effectiveness, but have proven to have insignificant outcomes on the bacterial pathogen.

Using clean seed, with little infection, has yielded effective results for researchers and producers. The pathogen, being seed-borne, can be controlled with the elimination of contaminated seed, however, clean seed is not always a sure solution. Because the pathogen may still live in the soil, the use of clean seed is only effective if both the soil and seed are free of the pathogen. Currently, there are no successful seed treatments available for producers to apply to wheat seed for the pathogen.

Variety resistance is another option for control of the disease. Using cultivars such as Blade, Cromwell, Faller, Howard or Knudson, which are resistant to BLS may reduce the impact of the disease and potentially break the disease cycle. Avoiding susceptible cultivars such as Hat Trick, Kelby, and Samson may also reduce the presence of the disease and reduce the amount of bacterial residue in the soil. Using integrated pest management techniques such as tillage to turn over the soil and bury the infection as well as rotating crops may assist with disease management, but are not a definitive control methods. Depending on conditions, the bacteria may survive for up to 81 months. Because the bacteria is moisture driven, irrigation may also increase the risks of BLS infection.

There is no resistance to Citrus Black Spot and once a tree has been infected there is no known cure causing tree removal to be the best option. Both Federal and State governments have recommended the following preventative measures.

To control "Guignardia citriparpa" fungicides like copper and/or strobilurins should be applied monthly from early May to the middle of September (in the northern hemisphere). Applications of the fungicides are recommended in early April (northern hemisphere) if that month has experienced more rainfall than usual resulting in the ideal conditions for citrus black spot to form.

Table 1. Recommended Chemical Controls for Citrus Black Spot

1)Lower rates can be used on smaller trees. Do not use less than minimum label rate.

2)Mode of action class for citrus pesticides from the Fungicide Resistance Action Committee (FRAC) 20111. Refer to ENY-624, "Pesticide Resistance and Resistance Management," in the 2012 Florida Citrus Pest Management Guide for more details.

3)Do not use more than 4 applications of strobilurin fungicides/season. Do not make more than 2 sequential applications of strobilurin fungicides.

Another method of control is to accelerate the leaf litter decomposition under the trees in citrus groves. Accelerating this decomposition reduces the chance for ascospore inoculation which generally takes place in the middle of March. There are three possible methods to hasten this decomposition. One method is the increase the mircrosprinkler irrigation in the grove to half an hour for at least five days of the week. This form of control should continue for about a month and a half. The second method is to apply urea or ammonium to the leaf litter. The last and final method to accelerate leaf decomposition is to apply lime or calcium carbonate to the litter. Urea, lime, and calcium carbonate reduce the number of fungal structures and spore production. Since the fungus requires wet conditions to thrive, air flow in the citrus grove should be maximized to reduce leaf wetness.

Along with these methods it is also important to get rid of debris such as fallen fruit or twigs in a manner that reduces the chances of infecting other plants. Citrus Black Spot can colonize and reproduce on dead twigs. To dispose of citrus debris it should either be heated to a minimum of 180℉ for two hours, incinerated, buried in a landfill, or fed to livestock. Plant trash should be moved with caution if at all to avoid spreading the infectious ascospores. Any trees that are infected with citrus black spot should be removed from the grove and disposed of. These trees must be removed because those that are declining and stressed will often have off season bloom. If there is more than one age of fruit present on the tree, it is possible for the asexual spores on the fruit to be transferred to new fruit, intensifying the disease. This off season blooming is often more problematic with Valencia oranges when old and new crops overlap.

There are multiple sources known to cause black gill disease. Poor pond conditions can cause debris to build up in the gills turning them black. Certain kinds of bacteria and the fungus genus Fusarium are also known causes.

Sugarcane smut or "Ustilago scitaminea Sydow" is caused by the fungus "Sporisorium scitamineum"; smut was previously known as "Ustilago scitaminea". The smut 'whip' is a curved black structure which emerges from the leaf whorl, and which aids in the spreading of the disease. Sugarcane smut causes significant losses to the economic value of a sugarcane crop. Sugarcane smut has recently been found in the eastern seaboard areas of Australia, one of the world's highest-yielding sugar areas.

For the sugarcane crop to be infected by the disease, large spore concentrations are needed. The fungi uses its "smut-whip" to ensure that the disease is spread to other plants, which usually occurs over a time period of three months. As the inoculum is spread, the younger sugarcane buds just coming out of the soil will be the most susceptible. Because water is necessary for spore germination, irrigation has been shown to be a factor in spreading the disease. Therefore, special precautions need to be taken during irrigation to prevent spreading of the smut.

Another way to prevent the disease from occurring in the sugarcane is to use fungicide. This can be done by either pre-plant soaking or post-plant spraying with the specific fungicide. Pre-plant soaking has been proven to give the best results in preventing the disease, but post-plant spraying is a practical option for large sugarcane cultivations.

Extensive treatments have been used on domestic animals more than on wild animals, probably because infected domestic animals are easier to identify and treat than infected wildlife. Treatment plans and management vary across taxa because this disease tends to affect each species differently. Antifungal drugs are the first line of defense to kill the agents causing phaeohyphomycosis, but despite the significant progress made in the last two decades and a 30% increase in available antifungal drugs since 2000, many drugs are not effective against black fungi. Diseases caused black fungi are hard to treat because the fungi are very difficult to kill. This high resilience may be contributed to the presence of melanin in their cell walls. Current antifungal agents the fungi are not resistant to are posaconazole, voriconazole, and azole isavuconazole.

In 2006, a free-living Eastern box turtle, "Terrapene carolina carolina", was found with a form of phaeohyphomycosis and was brought in the Wildlife Center of Virginia. Its symptom was swelling of the right hindfoot; it was diagnosed as having chromomycosis by histopathology. The center provided a series of antimicrobial treatments and a one-month course of 1 mg itraconazole, administered orally once a day. The eastern box turtle was euthanized due to further complications and the caretakers’ belief that the turtle would not be able to survive if placed back in the wild.

A recent case of a form of phaeohyphomycosis infection was found in a dog in 2011. The Journal of the American Veterinary Medical Association published a case study in which researchers successfully managed an intracranial phaeohyphomycotic fungal granuloma in a one-year-old male Boxer dog. Veterinarians of the Department of Veterinary Clinical Sciences at Tufts University surgically removed the granuloma in the right cerebral hemisphere. The patient was treated with fluconazole for 4 months, and was followed with voriconazole for 10 months. Both are medications used to treat fungal infections. Based on magnetic resonance imaging and cerebrospinal fluid (CSF) analysis 8 months after the surgery, the male Boxer’s outcome was considered excellent.

Emphasis has been placed on how to manage this disease through careful management practices including: proper handling, preventing crowding situation with animals, and transportation. Both the animals and the environment should be treated thoroughly to hinder the spread and control the fungal infection. This is especially important since humans can also contract this disease.

The genus Geosmithia (Ascomycota: Hypocreales) are generally saprophytic fungi affecting hardwoods. As of its identification in 2010, the species G. morbida is the first documented as a plant pathogen. The walnut twig beetle ("Pityophthorus juglandis") carries the mycelium and conidia of the fungus as it burrows into the tree. The beetle is currently only found in warmer climates, allowing for transmission of the fungus throughout the year. Generations of the beetle move to and from black walnut trees carrying the fungus as they create galleries, the adults typically moving horizontally, and the larvae moving vertically with the grain. As they move through the wood, the beetles deposit the fungus, which is then introduced into the phloem; cankers then develop around the galleries, quickly girdling the tree. The fungus has not been found to provide any value to the beetle. A study done by Montecchio and Faccoli in Italy in 2014 found that no fungal fruiting bodies were found around or on the cankers but in the galleries. Mycelium, and sometimes conidiophores and conidia were observed in the galleries as well. No sexual stage of the fungus has currently been found.

Velvet (in an aquarium environment) is usually spread by contaminated tanks, fish, and tools (such as nets or testing supplies). There are also rare reports of frozen live foods (such as bloodworms) containing dormant forms of the species. Frequently, however, the parasite is endemic to a fish, and only causes a noticeable "outbreak" after the fish's immune system is compromised for some other reason. The disease is highly contagious and can prove fatal to fish.

In order to control for the disease, the "Lymnaea" spp snails, which are the intermediate host for the liver flukes, need to be controlled. There are three ways that have proven most effective when controlling the snail populations:

- The first is by treating pastures and water channels with copper sulfate. This method is not always practical, because it is too expensive to treat in large areas. Lack of cooperation between neighbors is also a problem, snails are easily transported, and treated pastures become re-infested by neighboring fields and streams.

- Drenching the sheep with carbon tetra-chloride in paraffin oil has proven to be an alternative. However, drenching in more than recommended doses can be fatal, by causing liver damage, which could initiate the disease in sheep carrying "B. oedematiens" spores.

- Drainage is an effective option to eliminate the snails. However, draining the places where the grass grows eliminates a source of food for the sheep and creates other unwanted problems.

An escharotic is a substance that causes tissue to die and slough off. Examples include acids, alkalis, carbon dioxide, metallic salts and sanguinarine, as well as certain medicines like imiquimod. Escharotics known as black salves, containing ingredients such as zinc chloride and sanguinarine containing bloodroot extracts, were traditionally used in herbal medicine as topical treatments for localised skin cancers, but often cause scarring and can potentially cause serious injury and disfigurement. Consequently, escharotic salves are very strictly regulated in most western countries and while some prescription medicines are available with this effect, unauthorized sales are illegal. Some prosecutions have been pursued over unlicensed sales of escharotic products such as Cansema.

Some fish species serve as vectors for the disease and have subsequently spread the pathogen to other parts of the world. An example is the fathead minnow ("Pimephales promelas") which is responsible for the spread of redmouth disease to trout in Europe. Other vectors include the goldfish ("Carassius auratus"), Atlantic and Pacific salmon ("Salmo salar"), the emerald shiner ("Notropis atherinoides"), and farmed whitefish ("Coregonus" spp.). Infections have also occurred in farmed turbot ("Scophthalmus maximus"), seabass ("Dicentrarchus labrax"), and seabream ("Sparus auratus"). It can now be found in North and South America, Africa, Asia, and Australia, as well as Europe.

Blackleg, black quarter, quarter evil, or quarter ill () is an infectious bacterial disease most commonly caused by "Clostridium chauvoei", a Gram-positive bacterial species. It is seen in livestock all over the world, usually affecting cattle, sheep, and goats. It has been seen occasionally in farmed bison and deer. The acute nature of the disease makes successful treatment difficult, but an effective vaccine is available to provide animals with protective immunity.

The disease can tolerate warm or freezing temperature, but favorable conditions for the disease include wet and humid weather. Irrigated fields provide a favorable environment for the disease. The disease has become quite prevalent in semi-tropical regions, but can found all over the world where wheat is grown. Strong winds that blow soils help contribute to the spread of disease. When the spread is initiated by wind blown soil particles, symptoms will be found most readily towards the edges of the field.

Columnaris (also referred to as cottonmouth) is a symptom of disease in fish which results from an infection caused by the Gram-negative, aerobic, rod-shaped bacterium "Flavobacterium columnare". It was previously known as "Bacillus columnaris, Chondrococcus columnaris, Cytophaga columnaris" and "Flexibacter columnaris". The bacteria are ubiquitous in fresh water, and cultured fish reared in ponds or raceways are the primary concern – with disease most prevalent in air temperatures above 12–14 °C. It is often mistaken for a fungal infection. The disease is highly contagious and the outcome is often fatal. It is not zoonotic.

In affected orchards, new infections can be reduced by removing leaf litter and trimmings containing infected tissue from the orchard and incinerating them. This will reduce the amount of new ascospores released in the spring. Additionally, scab lesions on woody tissue can be excised from the tree if possible and similarly destroyed.

Chemical controls can include a variety of compounds. Benzimidazole fungicides, e.g., Benlate (now banned in many countries due to its containing the harmful chemical benzene) work well but resistance can arise quickly. A number of other chemical classes including sterol inhibitors such as Nova 40, and strobilurins such as Sovran are used extensively; however, some of these are slowly being phased out because of resistance problems.

Contact fungicides not prone to resistance, such as Captan, are viable choices. Potassium bicarbonate is an effective fungicide against apple scab, as well as powdery mildew, and is allowed for use in organic farming. Copper and Bordeaux mixture are traditional controls but are less effective than chemical fungicides, and can cause russeting of the fruit. Wettable sulfur also provides some control. Timing of application and concentration varies between compounds.

An apple scab prognostic model called RIMpro was developed by Marc Trapman, which numerically grades infection risk and can serve as a warning system. It allows better targeted spraying. Parameter for calculation are wetness of leaves, amount of rain fall and temperature.

Fifteen genes have been found in apple cultivars that confer resistance against apple scab. Researchers hope to use cisgenic techniques to introduce these genes into commercial cultivars and therefore create new resistant cultivars. This can be done through conventional breeding but would take over 50 years to achieve.

Phaeohyphomycosis is a disease caused by this fungus. If given the opportunity, this disease can spread to the brain and cause a painful death. There have been multiple reports of this host of fungi, but by the time the disease is recognized, it is usually too late for the animal to be successfully treated. Recent searches of databases show that there are no current projects studying the spread of this fungus in wild animals, though there are documented cases of its occurrence.

In 2005, a five-month-old snow leopard ("Uncia uncia") in Europe was diagnosed with phaeohyphomycosis due to "Cladophalophora bantiana". This fungus caused spastic paralysis as well as the inability to defecate or urinate. Because of this finding, more researchers are aware of this disease and the fact that it does not just infect the brain, as previously thought, but also other organs and other parts of the nervous system. A Purdue University study in 2011 showed a Huacaya alpaca ("Vicugna pacos") with the same fungus affected by cerebral phaeohyphomycosis. The eight-year-old animal was the first report of this disease in a camelid ruminant.

Conclusively, phaeohyphomycosis is a highly prolific disease that is caused by multiple genera of fungi. The disease is transmissible through several mediums, including air, wind, and water. Both individual animals and whole populations can be affected by it. Although it does not seem to be an epidemic, it is nonetheless an area of concern and requires much more active research rather than simply reports of terminal or already-dead animals.

The smuts are multicellular fungi characterized by their large numbers of teliospores. The smuts get their name from a Germanic word for dirt because of their dark, thick-walled, and dust-like teliospores. They are mostly Ustilaginomycetes (of the class Teliomycetae, subphylum Basidiomycota) and can cause plant disease. The smuts are grouped with the other basidiomycetes because of their commonalities concerning sexual reproduction.

Smuts are cereal and crop pathogens that most notably affect members of the grass family ("Poaceae"). Economically important hosts include maize, barley, wheat, oats, sugarcane, and forage grasses. They eventually hijack the plants' reproductive systems, forming galls which darken and burst, releasing fungal teliospores which infect other plants nearby. Before infection can occur, the smuts need to undergo a successful mating to form dikaryotic hyphae (two haploid cells fuse to form a dikaryon).

Grapevine trunk diseases (GTD) are the most destructive diseases of vineyards worldwide. Fungicides (such as sodium arsenite or 8-hydroxyquinoline, used to fight esca) with the potential to control GTD have been banned in Europe and there are no highly effective treatments available. Action to develop new strategies to fight these diseases are needed.

The following fungal species are responsible for grapevine trunk diseases:

- "Botryosphaeria dothidea" and other "Botryosphaeria" species, such as , "B. obtusa", "B. parva" and "B. australis",

- "Cylindrocarpon" spp., "Ilyonectria" spp., "Dactylonectria" spp. and "Campylocarpon" spp.(cause of black foot disease)

- "Diplodia seriata" (cause of bot canker)

- "Diplodia mutila" (cause of Botryosphaeria dieback)

- "Dothiorella iberica"

- "Dothiorella viticola"

- "Eutypa lata" (cause of Eutypa dieback)

- "Fomitiporia mediterranea" (cause of esca)

- "Lasiodiplodia theobromae" (cause of Botryosphaeria dieback)

- "Neofusicoccum australe"

- "Neofusicoccum luteum"

- "Neofusicoccom parvum"

- "Phaeoacremonium minimum" (cause of esca and Petri disease) and other "Phaeoacremonium" species

- "Phaeomoniella chlamydospora" (cause of esca and Petri disease)