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.

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.

Sulfonamides are the traditional remedies to paracoccidiodomycosis. They were introduced by Oliveira Ribeiro and used for more than 50 years with good results. The most-used sulfa drugs in this infection are sulfadimethoxime, sulfadiazine, and co-trimoxazole. This treatment is generally safe, but several adverse effects can appear, the most severe of which are the Stevens-Johnson syndrome and agranulocytosis. Similarly to tuberculosis treatment, it must be continued for up to three years to eradicate the fungus, and relapse and treatment failures are not unusual.

Antifungal drugs such as amphotericin B or itraconazole and ketoconazole are more effective in clearing the infection, but are limited by their cost when compared with sulfonamides.During therapy, fibrosis can appear and surgery may be needed to correct this. Another possible complication is Addisonian crisis. The mortality rate in children is around 7-10%.

Plant varieties that are resistant to "Armillaria" or species are resistant to other environmental or biological stressors. If the infected area has been cleared of trees, plants that are not vulnerable to the disease should be planted for five or so years until "Armillaria" is eradicated. Stump removal is also an effective management tool but can be expensive. Another way to reduce susceptibility is to maintain plant health by regular fertilization (if needed), watering during droughts, and trying not to create wounds on the plant. Fumigation can also be used to reduce the amount of inoculum.

Necrotic ring spot can be managed through chemical and cultural controls. Cultural control includes the use of ammonium sulfate or other acidifying fertilizers to suppress the pathogen by lowering the pH of the soil to between 6.0 and 6.2. The more acidic soil discourages the activity of "O. korrae" (9) When reducing pH to these levels, additional manganese applications should be undertaken to compensate for lower pH. As of now, there are only two resistant cultivars of bluegrass, which are ‘Riviera’, and ‘Patriot’ (9). One component of their resistance could be that they are tolerant to low temperature, because the grass is more susceptible to the pathogen under colder temperatures(8). In addition, reducing watering inputs and growing turf on well drained soils can lessen disease symptoms.

Many different fungicides are used to control the pathogen, Fenarimol, Propiconazole, Myclobutanil, and Azoxystrobin (8). Historically, Fenarimol and Myclobutanil were predominantly used (14). In a study where diluted pesticides were sprayed throughout infested test plots, Fenarimol was found to be the most effective with a 94.6% reduction of the disease. Myclobutanil also decreased the amount of disease, but only by 37.7% (8). Myclobutanil is generally recognized as a very weakly acting demethylation inhibitor (DMI) fungicide and fenarimol is no longer registered for turf so a number of other DMI fungicides have been employed successfully, including Propiconazole, Tebuconazole, Metconazole and others. Pyraclostrobin and Fluoxastrobin have also been used to control the pathogen.

No vaccine is available. Simple hygienic precautions like wearing shoes or sandals while working in fields, and washing hands and feet at regular intervals may help prevent the disease.

no approved human vaccine exist against "Dermatophytosis". For horses, dogs and cats there is available an approved inactivated vaccine called "Insol Dermatophyton" (Boehringer Ingelheim) which provides time-limited protection against several trichophyton and microsporum fungal strains.

If mucormycosis is suspected, amphotericin B therapy should be immediately administered due to the rapid spread and high mortality rate of the disease. Amphotericin B is usually administered for an additional 4–6 weeks after initial therapy begins to ensure eradication of the infection. Isavuconazole was recently FDA approved to treat invasive aspergillosis and invasive mucormycosis.

After administration of either amphotericin B or posaconazole, surgical removal of the "fungus ball" is indicated. The disease must be monitored carefully for any signs of reemergence.

Surgical therapy can be very drastic, and in some cases of disease involving the nasal cavity and the brain, removal of infected brain tissue may be required. In some cases surgery may be disfiguring because it may involve removal of the palate, nasal cavity, or eye structures. Surgery may be extended to more than one operation. It has been hypothesized that hyperbaric oxygen may be beneficial as an adjunctive therapy because higher oxygen pressure increases the ability of neutrophils to kill the organism.

Zygomycosis has been found in survivors of the 2004 Indian Ocean earthquake and tsunami and in survivors of the 2011 Joplin, Missouri tornado.

The term oomycosis is used to describe oomycete infections. These are more common in animals, notably dogs and horses. These are heterokonts, not true fungi. Types include pythiosis (caused by "Pythium insidiosum") and lagenidiosis.

Zygomycosis has been described in a cat, where fungal infection of the tracheobronchus led to respiratory disease requiring euthanasia.

Drugs like ketoconazole,

voriconazole, and itraconazole are generally employed in treating the infection. Actinomycetes usually respond well to medical treatment, but the eumycetes are generally resistant and may require surgical interventions including amputation.

Treatment requires both systemic oral treatment with most of the same drugs used in humans—terbinafine, fluconazole, or itraconazole—as well as a topical "dip" therapy.

Because of the usually longer hair shafts in pets compared to those of humans, the area of infection and possibly all of the longer hair of the pet must be clipped to decrease the load of fungal spores clinging to the pet's hair shafts. However, close shaving is usually not done because nicking the skin facilitates further skin infection.

Twice-weekly bathing of the pet with diluted lime sulfur dip solution is effective in eradicating fungal spores. This must continue for 3 to 8 weeks.

Washing of household hard surfaces with 1:10 household sodium hypochlorite bleach solution is effective in killing spores, but it is too irritating to be used directly on hair and skin.

Pet hair must be rigorously removed from all household surfaces, and then the vacuum cleaner bag, and perhaps even the vacuum cleaner itself, discarded when this has been done repeatedly. Removal of all hair is important, since spores may survive 12 months or even as long as two years on hair clinging to surfaces.

Paracoccidioidomycosis has been reported as an autochthonous disease from southern Mexico to northern Argentina. No cases have been reported from Belize and Nicaragua in Central America, or from Chile, French Guiana, Guiana, and Suriname in South America. Paracoccidioidomycosis is prevalent in Brazil, Colombia, Venezuela, and Argentina, and is classically associated with individuals from rural areas. The typical patient is a man aged 30 to 50 years.

Fumagillin has been used in the treatment.

Another agent used is albendazole.

Due to the effectiveness of fungicide application and it’s relatively minor damage to crops, there are few cultural controls and no resistant peach variants that have been developed for the current market. For prevention of peach scab, proper pruning of leaves to allow adequate sunlight will drastically reduce the risk of infection and propagation. The primary form of regulation for peach scab requires frequent applications of commercial fungicides. There are three main types of fungicides that are effective against peach scab: captan, chlorothalonil, and demethylation inhibitors. Proper use of chlorothalonil requires application starting from shuck split and reapplication every two weeks. Increased temperature and wet weather will necessitate more frequent applications. Applications are necessary until 4–6 weeks until harvest.

Not every hospital in the USA are required to publicize details of infectious outbreaks which occur within their facilities. In 2014, details of a lethal mucormycosis outbreak which occurred in 2008 emerged after television and newspaper reports responded to an article in a pediatric medical journal. Contaminated hospital linen was found to be spreading the infection.

A cluster of infections occurred in the wake of the 2011 Joplin tornado. As of July 19, a total of 18 suspected cases of cutaneous mucormycosis had been identified, of which 13 were confirmed. A confirmed case was defined as 1) necrotizing soft-tissue infection requiring antifungal treatment or surgical debridement in a person injured in the tornado, 2) with illness onset on or after May 22 and 3) positive fungal culture or histopathology and genetic sequencing consistent with a Mucormycete. No additional cases related to that outbreak have been reported since June 17. Ten patients required admission to an intensive-care unit, and five died.

Cutaneous mucormycosis has been reported after previous natural disasters; however, this is the first known cluster occurring after a tornado. None of the infections were found in persons cleaning up debris; instead it is believed transmission occurred through penetrating injuries inflicted by contaminated objects (e.g. splinters from a woodpile).

The best way to manage SDS is with a resistant variety. One issue is that most resistant varieties are only partially resistant so yield reductions may still occur. Another issue is that the plant needs resistance for SDS and SCN in order to gain true resistance because of their synergistic relationship and most varieties do not have resistance for both. Aside from resistance, the only other ways to control SDS are management practices.

These include:

- Avoid planting in cool, wet conditions

- Plant later when the soil has warmed up

- Try avoiding soil compaction as it creates wet spots in the soil that can increase plant stress and SDS infection rates

- Managing for SCN as this nematode often occurs alongside "F. virguliforme"

- Deep tillage to break up compaction and help the soil warm faster

One common management tactic used in other pathogen management plans is crop rotation. In some cases, disease severity can be reduced but most often it is not effective. This is because of chlamydospores and macroconidia as they can persist in soils for many years.

Fungicides are another common product used to control fungal pathogens. In-furrow applications and seed treatments with fungicides have some effect in decreasing disease instance but in most cases, the timing isn't right and the pathogen can still infect the plants. Foliar applications of fungicides have no effect on disease suppression for SDS because the fungi are found in the soil and mainly the roots of the plants. Most foliar fungicides do not move downward through plants, therefore having no effect on the pathogen.

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.

The blotches are cosmetic damage "unacceptable to consumers" and downgrade fruit from premium fresh-market grade to processing use, i.e. reduce its market value, but leaf and fruit development are not affected.

"W. carpophilus" can remain viable for several months and spores are often airborne. Since the fungi thrive in wet conditions, overhead watering should be avoided. Remove and dispose of any infected buds, leaves, fruit and twigs. In fall, fixed copper or Bordeaux mixture can be applied.

Shot hole disease is a major concern of the stone fruit industry. It is estimated that 80% of the California almond crop may be infested with shot hole disease, resulting in a potential yield loss of 50-75%. In the 1930s, it was found that applications of Bordeaux mixture reduces shot hole disease on peaches from 80% to 9%.

Preventive measures are pruning which allows light and air to enter the tree, to achieve fast drying. Strong growth within the root area dams up moisture and facilitates infection.

A prognostic model called Sooty Blotch RIMpro has been developed, which still awaits validation. Similar to the apple scab model it numerically grades risk and degree of infection and can serve as a warning system. It allows conventional growers to spray more targeted. The parameters for calculation are wetness of leaves, amount of rain fall and temperature.

Conventional orchards that spray fungicides against apple scab, treat soot blotch and flyspeck at the same time. Therefore, the problem is not seen in conventional non-resistant varieties. However, scab-resistant varieties, which are not sprayed frequently show the infection. In organic orchards, spraying 4–5 with lime sulphur or coco soap during the main infectious periods is recommended.

Because fungi prefer warm, moist environments, preventing ringworm involves keeping skin dry and avoiding contact with infectious material. Basic prevention measures include:

- Washing hands after handling animals, soil, and plants.

- Avoiding touching characteristic lesions on other people.

- Wearing loose-fitting clothing.

- Practicing good hygiene when participating in sports that involve physical contact with other people.

There are a few controls for beech bark disease. One important management strategy is prohibiting the movement of nursery stock or other materials that may harbor the beech scale insect. Insecticides, generally not applied under forest conditions, are primarily used on high-value ornamental trees. The use of other organisms as controls is also a possibility. The ladybird beetle is a beetle that preys on the beech scale insect. A fungus that parasitizes the "Neonectria" fungus could also be employed. The problem with using these organisms to control beech bark disease is that their impact on the disease has not been evaluated extensively. In a forest setting, controlling the beech bark disease is too costly. Timely salvage cutting can reduce economic losses of beech in a forest. In stands where beech bark disease is established, silvicultural best practice is to retain large overstory trees which show visual resistance (no scale, cankers or fungus), remove heavily infested/dying trees and then treat sprouts from infested trees with herbicides. The residual, resistant parent trees are future sources of resistant seed/sprouts. Resistance to beech bark disease in a stand may be 1%-5% of trees or more, with significant regional variation. A study of 35 sites in three Canadian provinces found resistance rates ranging from 2.2%-5.7%.

Keeping the skin clean and dry, as well as maintaining good hygiene, will help larger topical mycoses. Because fungal infections are contagious, it is important to wash after touching other people or animals. Sports clothing should also be washed after use.