Black pod disease is caused by many different "Phytophthora spp." pathogens all expressing the same symptoms in cocoa trees ("Theobroma cacao"). This pathogen if left untreated can destroy all yields; annually the pathogen can cause a yield loss of up to 1/3 and up to 10% of total trees can be lost completely. With the value of the cocoa industry throughout the world being so large there are much research and control efforts that go into these "Phytophthora spp." pathogens.

This pathogen can be located anywhere on the cocoa trees but is most noted for the black mummified look it will give to the fruit of the cocoa tree. Staying ahead of the pathogen is the best means of control, the pathogen can be greatly reduced if leaf litter is not allowed to stay on the ground and if the pathogen gets out of hand chemical control can be used. This pathogen is mostly found in tropical areas where the cocoa trees are located and need rainfall in order to spread its spores.

The disease affect most stone plants including peaches, apricots and plums. The symptoms can generally be found in three major parts of plant: fruits, twigs, and leaves. The symptoms on leaves and twigs are often considered as the least notable. Infected leaves initially show small and green colored lesions on under the leaves. They progress into yellowish brown and eventually appear as dark brown or black spots.

Twig lesions start to form on green young stems. The lesions are about 3 up to 6.5 mm in diameter size. They usually first have reddish brown colors then which will turn into darker colors as they enlarge to an oval shape of 3 x 6mm approximately.

About six weeks after petals are fallen, the first and most notable and serious symptoms appear on fruits. Spots, which generally range from 1 to 2 mm in diameter size, are formed on the end of stem. They gradually change its color into dark green or black and grow about few millimeters in diameter. As they enlarge, yellow circles will form around the velvety dark green spots. The spots have raised appearance on fruits instead of sunken figures which can be found most prevalently in other fungal infections. In some severe cases, fruits may be stunted or opened and exposed to further infection by airborne microorganisms.

Adult walnut twig beetles carry spores of the "Geosmithia morbida" fungus, which grows profusely around the pupal chamber of the beetles. Following emergence from trees the beetles subsequently tunnel into branches and trunks of walnut for production of egg galleries or overwintering shelters. The fungus is introduced into the tree during this wounding where it subsequently germinates and grows.

The fungal mycelium initially colonize tissue immediately surrounding the beetle galleries. However, in less than a month black, oval-shaped, inky cankers extend considerably beyond the galleries and may reach more than 3 cm in length in susceptible hosts (e.g., black walnut). In the beginning these cankers develop in phloem and tissues formed by the cork cambium. The affected area is very shallow and never show the ‘open-faced’, perennial, target-shape typical of many canker diseases of trees (e.g., Nectria canker). Instead in TCD the bark remains firmly attached to the canker face making the necrotic areas very difficult to observe. Branch cankers usually are not visible until the outer bark is shaved to expose the beetle tunnels, although during late stages of the disease a dark amber stain may form on the bark surface in association with the cankers.

Each time a beetle tunnels into a tree a canker is initiated. Cankers also may continue to expand and penetrate into the cambium of the tree. Each such injury destroys the phloem and robs the tree of its ability to store and move nutrients. As TCD progresses cankers coalesce to further girdle branches greatly restricting nutrient movement. As the tree declines, more bark beetles are attracted and more cankers are formed.

Eventually the enormous number of beetle attacks and subsequent canker formation overwhelms and kills the tree. Thousand cankers is a progressive disease and its effects result from the culmination of a large number of relatively small cankers over a period of time. Just as a thousand cuts was once used as a form of human execution in Imperial China, black walnuts are subjected to death by thousands of branch and trunk cankers produced by infection from the "Geosmithia" fungus.

In end stages of the disease external symptoms become visible. Leaf yellowing on the exterior of the crown is often the first symptom and may originally be restricted to a single branch. However, as the cumulative effects of the girdling progress increasingly large areas of the tree are affected. Sudden leaf wilting, ultimately involving large limbs, characterizes end stage thousand cankers disease. In susceptible hosts, trees are almost always killed within 2–3 years after external symptoms of leaf yellowing are first observed.

The progress of thousand cankers will vary due to several factors, notably the susceptibility of the host. There appears to be a considerable range of TCD susceptibility among various "Juglans" species with "Juglans nigra" (black walnut) being particularly susceptible. Conversely, Arizona walnut ("Juglans major") appears to be quite resistant to the disease, with bark beetle attacks largely limited to small diameter branches, the fungus growing to a very limited extent, and effects of the disease rarely, if ever, progressing to involve large areas of the tree. Similarly southern California walnut ("Juglans californica") and little walnut ("Juglans microcarpa") may show fairly high resistance. Northern California walnut ("Juglans hindsii") and the commercial nut-producing Persian (English) walnut ("Juglans regia") apparently show various degrees of intermediate TCD susceptibility.

Citrus Black Spot is a fungal disease caused by Guignardia citricarpa. This Ascomycete fungus affects citrus plants throughout subtropical climates, causing a reduction in both fruit quantity and quality. Symptoms include both fruit and leaf lesions, the latter being critical to inter-tree dispersal. Strict regulation and management is necessary to control this disease since there are currently no citrus varieties that are resistant.

Peach scab, also known as peach freckles, is a disease of stone fruits caused by the fungi "Cladosporium carpophilum". The disease is most prevalent in wet and warm areas especially southern part of the U.S. as the fungi require rain and wind for dispersal. The fungus causes scabbing, lesions, and defoliating on twig, fruit, and leaf resulting in downgrade of peach quality or loss of fruits due to rotting in severe cases.

Common spot of strawberry is one of the most common and widespread diseases of strawberry. Common spot of strawberry is caused by the fungus Mycosphaerella fragariae (imperfect stage is "Ramularia tulasnei"). Symptoms of this disease first appear as circular, dark purple spots on the leaf surface. "Mycosphaerella fragariae" is very host specific and only infects strawberry.

Mycosphaerella fragariae is a species from family Mycosphaerellaceae.

Ascochyta blights occur throughout the world and can be of significant economic importance. Three fungi contribute to the ascochyta blight disease complex of pea ("Pisum sativum"). "Ascochyta pinodes" (sexual stage: "Mycosphaerella pinodes") causes Mycosphaerella blight. "Ascochyta pinodella" (synonym: "Phoma medicaginis" var. "pinodella") causes Ascochyta foot rot, and "Ascochyta pisi" causes Ascochyta blight and pod spot. Of the three fungi, "Ascochyta pinodes" is of the most importance. These diseases are conducive under wet and humid conditions and can cause a yield loss of up to fifty percent if left uncontrolled. The best method to control ascochyta blights of pea is to reduce the amount of primary inoculum through sanitation, crop-rotation, and altering the sowing date. Other methods—chemical control, biological control, and development of resistant varieties—may also be used to effectively control ascochyta diseases.

Apple scab is a disease of "Malus" trees, such as apple trees, caused by the ascomycete fungus "Venturia inaequalis". The disease manifests as dull black or grey-brown lesions on the surface of tree leaves, buds or fruits. Lesions may also appear less frequently on the woody tissues of the tree. Fruits and the undersides of leaves are especially susceptible. The disease rarely kills its host, but can significantly reduce fruit yields and fruit quality. Affected fruits are less marketable due to the presence of the black fungal lesions.

Thousand cankers disease is a recently recognized disease of certain walnuts ("Juglans" spp.). The disease results from the combined activity of the walnut twig beetle ("Pityophthorus juglandis") and a canker producing fungus, "Geosmithia morbida". Until July 2010 the disease was only known to the western United States where over the past decade it has been involved in several large scale die-offs of walnut, particularly black walnut, "Juglans nigra". However, in late July 2010 a well-established outbreak of the disease was found in the Knoxville, Tennessee area. This new finding is the first locating it within the native range of its susceptible host, black walnut.

Certain techniques can be used to determine which pathogen is causing disease. One standard technique for distinguishing strains is microscopy. Under a microscope, "M. pinodes" can be diagnosed by the presence of pseudothecia. "P pinodella" can be diagnosed by the size of conidia produced. "P. pinodella" produces conidia that are smaller than the conidia of "M. pinodes" or "A. pisi". "A. pisi" can be diagnosed by the color of the conidia. In comparison to the light colored, buff spore masses of "M. pinodes" and "P. pinodella" produced on oatmeal agar, "A. pisi" spores masses are carrot red.

Other techniques for diagnosis involve serological assays, isoenzyme analysis, restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPD) assays, and by using monoclonal antibodies.

Sudden Death Syndrome (SDS) in Soybean plants quickly spread across the southern United States in the 1970s, eventually reaching most agricultural areas of the US. SDS is caused by a Fusarium fungi, more specifically the soil borne root pathogen "Fusarium virguliforme," formerly known as "Fusarium solani" f. sp. "glycines"."." Losses could exceed hundreds of millions of dollars in US soybean markets alone making it one of the most important diseases found in Soybeans across the US

Most of the SDS symptoms can be confused with other factors like nutrient deficiencies and some other diseases like brown stem rot and stem canker. Usually the first symptom seen is interveinal chlorosis, which is the yellowing of the plant material between the leaf veins. When leaves begin to die, puckering and mottling can also be observed along with the chlorosis. As severity increases, necrosis (death of cells) occurs and eventually these leaves will fall off, leaving only petioles left on the stem. If the conditions are right (cool and wet), these symptoms can appear suddenly, causing large yield reductions. Normally, this is seen in mid or late July around the time of flowering and pod production.

In addition to foliar symptoms, the stem of the soybean plant can show symptoms as well. If a soybean stem with SDS is split, the pith will be visibly white while the cortical tissue around the pith will be tan to light brown in color. If the pith is brown in color (or if the whole stem looks brown on the inside), it is likely that the plant has brown stem rot, rather than SDS

Along with the above ground foliar and stem symptoms, the roots usually show some kind of rotting and decrease in vigor compared to other healthy soybean roots. If soil conditions are moist, roots are also likely to show blue masses of spores (macroconidia) around the taproot just below the soil surface. Blue fungal masses, found along with the foliar and stem symptoms, are strong diagnostic indicators for SDS

False melanose lesions are characterized by many small, tan, slightly raised lesions. The lesions are much smaller than the hard spot variety with an average diameter of less than 1 mm (.04 in).

They are found on unripe fruit and are difficult to observe later in the season. Unlike hard spot lesions, no pycnidia are present.

Bacterial leaf streak (BLS), also known as black chaff, is a common bacterial disease of wheat. The disease is caused by the bacterial species "Xanthomonas translucens" pv. undulosa. The pathogen is found globally, but is a primary problem in the US in the lower mid-south and can reduce yields by up to 40 percent. BLS is primarily seed-borne (the disease is transmitted by seed) and survives in and on the seed, but may also survive in crop residue in the soil in the off-season. During the growing season, the bacteria may transfer from plant to plant by contact, but it is primarily spread by rain, wind and insect contact. The bacteria thrives in moist environments, and produces a cream to yellow bacterial ooze, which, when dry, appears light colored and scale-like, resulting in a streak on the leaves. The invasion of the head of wheat causes bands of necrotic tissue on the awns, which is called Black Chaff.

The disease is not easily managed, as there are no pesticides on the market for treatment of the infection. There are some resistant cultivars available, but no seed treatment exists. Some integrated pest management (IPM) techniques may be used to assist with preventing infection although, none will completely prevent the disease.

This disease affects strawberry plant foliage causing purple spots ⅛ to ¼ inches across on the upper side of the leaves. At first, the whole spot is purple but as the disease matures the center of the leaf spots become tan or gray, then almost white. When numerous spots merge foliage death can occur; this can stunt or kill infected plants when severe.

On petioles, stolons, calyxes, and fruit trusses, elongated lesions may form and interfere with water transport in the plant, weakening the plant and making it more susceptible to invasion by a secondary organism.

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).

Bacterial leaf streak is a pathogen known to infect and damage wheat varieties. The pathogen has also been known to infect other small grain all cereal crops such as rice, barley and triticale. The strains of the pathogen are named differently according to the species they infect. It is one of the most destructive diseases in rice.

Resistant wheat cultivars offer the best protection against yield loss, but little is known about the inheritance of resistance. The disease is most common on wheat and can be found on winter and summer wheat varieties.

Symptoms of this pathogen can be seen on the stem, leaves, and glumes. Stem symptoms are not always present, but can be seen as a dark brown to purple discoloration on the stem below the head and above the flag leaf. In the early stages of the disease, translucent water soaked streaks can be seen on the leaves often accompanied by a shiny glaze or clumps of dried bacteria on the leaf surface. These markings turn to brown lesions after just a few days, and may be surrounded by a lime green halo. Lesions can stretch the entire leaf blade.

BLS exhibits similar symptoms to those of "Septoria nodorum", a common fungal infection. A common sign that will distinguish this pathogen from "Septoria nodorum" is the lack of spores on the leaves, which appears as tiny black spots on the leaf surface with a "Septoria" infection. A cream to yellow colored bacterial ooze produced by BLS infected plant parts is also a distinguishing sign of the pathogen.

Infected glumes, known as black chaff, are darkened and necrotic. Severe symptoms will result in kernels that are discolored due to black and purple streaks. Plants infected with bacterial leaf streak will exhibit an orange cast from leaf symptoms and suffer yield and quality loss.

Black band disease is a coral disease in which corals develop a black band. It is characterized by complete tissue degradation due to a pathogenic microbial consortium. The mat is present between apparently healthy coral tissue and freshly exposed coral skeleton.

Black band disease was first observed on reefs in Belize in 1973 by A. Antonius, who described the pathogen he found infecting corals as "Oscillatoria membranacea", one of the cyanobacteria. The band color may be blackish brown to red depending on the vertical position of a cyanobacterial population associated with the band. The vertical position is based on a light intensity-dependent photic response of the cyanobacterial filaments, and the color (due to the cyanobacterial pigment phycoerythrin) is dependent on the thickness of the band. The band is approximately thick and ranges in width from to White specks may be present on surface, at times forming dense white patches. The pathogenic microbial mat moves across coral colonies at rates from to a day. Tissue death is caused by exposure to an hypoxic, sulfide-rich microenvironment associated with the base of the band.

It has been observed in spiny lobsters ("Panulirus ornatus") in Vietnam, where it is caused by a species of "Fusarium".

It has been observed in shrimp, where the agent is microscopic protozoan "Hyalophysa chattoni" or a close relative, in Galveston Bay, Texas and other locations.

The symptom of black pod disease is the necrotic lesion on the cocoa pod with brown or black color, which eventually enlarged to cover the whole pod. White mycelia growth on lesions that appeared several days after infection is the sign for the causal pathogen of black pod disease, which is "Phytophthora spp".

Black pod disease starts when the infected pod shows some little yellow spots, which eventually turn brown and enlarge to a dark brown or black lesion within five days. The lesion is fast growing and covers the entire pod after eighth day of infection. The infection does not only occur on the pod surface, but also invades inside the pod affecting the beans. The growth of white mycelia on black pod is visible after 11 days and the sporulation is initiated. The dispersal of sporangia or zoospores through water, ants and other insects occurs at this stage and will infect other healthy pods nearby. Direct contact of a black pod with healthy pods also leads to the spread of disease. In addition, the infected flower cushion and mummified pods are the locations for "P. palmivora" survival during dry season, where the pathogen will grow and continue to infect other developing pods

The infection occurs on any stage of pod development, where it causes wilting and dying of young pods and destroyed the beans of mature pods. The fully infected pods (the mummified pod), which then become dehydrated, are capable of providing the inoculum of "P. palmivora" for at least 3 years. "P. megakarya" causes the same symptom as "P. palmivora", but the occurrence is faster and generally produces greater amount of spores. Both "P. palmivora" and "P. megakarya" also caused canker on bark, flower cushion and chupons, and cankers on the base could extend to the main roots. Cankers were identified as one of inoculum sources for black pod disease. Furthermore, the pattern of infection caused by "P. megakarya" starts from the ground and moves up to the canopy, however there is no distinct pattern of disease infection caused by "P. palmivora" was reported. This pattern of infection could be due to "P. megakarya" and "P. palmivora" that were found to survive in soil and "P. megakarya" could be surviving in the roots of a few species of shade trees found in cocoa plantation.

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)

Skeletal eroding band (SEB) is a disease of corals that appears as a black or dark gray band that slowly advances over corals, leaving a spotted region of dead coral in its wake. It is the most common disease of corals in the Indian and Pacific Oceans, and is also found in the Red Sea.

So far one agent has been clearly identified, the ciliate "Halofolliculina corallasia". This makes SEB the first coral disease known to be caused by a protozoan. When "H. corallasia" divides, the daughter cells move to the leading edge of the dark band and produce a protective shell called a lorica. To do this, they drill into the coral's limestone skeleton, killing coral polyps in the process.

A disease with very similar symptoms has been found in the Caribbean Sea, but has been given a different name as it is caused by a different species in the genus "Halofolliculina" and occurs in a different type of environment.

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.

Human’s clinical signs consisted of swelling and eye infections. There were nodules underneath the skin, abscesses or cysts, and lesions running throughout the body. There were papules, plaques and granulomatous damages on the body. In extreme cases there were deep infections within the eyes, bones, heart and central nervous system.