There are a number of control methods to prevent and reduce the Banana Freckle disease. The paper bag method seems to be the most effective way to gain physical control of the pathogen. The infected leaves are the primary source of spores, and placing a bag over the bananas, once harvested, creates a barrier to prevent inoculum from spreading to the fruit.

Some cultural controls include pruning out infectious plant material, planting in pathogen-free fields, and practicing proper sanitation techniques. In the Philippines, pruning and cutting out patches of infected tissue have prevented the spread of the pathogen in the plant during disease outbreaks. General sanitation practices have also reduced the spread of inoculum. When planters failed to maintain sanitary equipment, seeds, and soil, they witnessed severe fruit infections. The more freckles seen on the leaves of the plant, the more the fruit develops symptoms of the disease. Inversely, less freckles corresponded to less disease.

In addition, multiple fungicides have been seen to reduce Banana Freckle disease. In Hawaii, spraying the leaves and fruit with maneb (1 lb./100 gal water plus 4 oz of sticker-spreader) every 2 weeks or once a month throughout the year has remarkably reduced the spread of inoculum. In Taiwan, spraying fungicides, such as phaltan, orthocide, chlorothalonil, dithiocarbamates, and propiconazole, biweekly have produced effective results against the disease. In the Philippines, chemical controls used against Black or Yellow Sigatoka disease have been helpful. These consist of mancozeb, triazoles, tridemorph, and strobilurin. Mancozeb seems to be the most effective fungicide against Banana Freckle disease in Hawaii and the Philippines . These fungicides do not eliminate the pathogen completely, but they reduce the inoculum levels and eventually reduce yield loss.

Lastly, eradication of infected plants can prevent further infection of other fruit around the area.

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.

The first strategy of management is the cultural practices for reducing the disease. It includes adequating row and plant spacing that promote better air circulation through the canopy reducing the humidity; preventing excessive nitrogen on fertilization since nitrogen out of balance enhances foliage disease development; keeping the relatively humidity below 85% (suitable on greenhouse), promote air circulation inside the greenhouse, early planting might to reduce the disease severity and seed treatment with hot water (25 minutes at 122 °F or 50 °C).

The most effective and widespread method of disease control is to use resistant cultivars. However, only few resistant cultivar to tomato leaf mold are known such as Caruso, Capello, Cobra (race 5), Jumbo and Dombito (races 1 and 2). Moreover, this disease is not considered an important disease for breeding field tomatoes.

Breeding resistant varieties is the most cost-effective method to control this rust. Fungicides are available but vary in availability depending on their registration restrictions by national or state governments. Development of varieties resistant to the disease is always an important objective in wheat breeding programs for crop improvement. These resistance genes, however, became ineffective due to the acquisition of virulence to that particular resistance gene rendering the variety susceptible.

Burying the debris under the last year’s crop will help in reducing the presence of "Cercospera zeae-maydis", as the fungal-infected debris can only survive above the soil surface. Again this technique will aid in reducing the primary inoculum, but it will not completely eradicate the disease.

"F. oxysporum" is a major wilt pathogen of many economically important crop plants. It is a soil-borne pathogen, which can live in the soil for long periods of time, so rotational cropping is not a useful control method. It can also spread through infected dead plant material, so cleaning up at the end of the season is important.

One control method is to improve soil conditions because "F. oxysporum" spreads faster through soils that have high moisture and bad drainage. Other control methods include planting resistant varieties, removing infected plant tissue to prevent overwintering of the disease, using soil and systemic fungicides to eradicate the disease from the soil, flood fallowing, and using clean seeds each year. Applying fungicides depends on the field environment. It is difficult to find a biological control method because research in a greenhouse can have different effects than testing in the field. The best control method found for "F. oxysporum" is planting resistant varieties, although not all have been bred for every forma specialis.

"F. oxysporum" f. sp. "batatas" can be controlled by using clean seed, cleaning up infected leaf and plant material and breeding for resistance. Fungicides can also be used, but are not as effective as the other two because of field conditions during application. Fungicides can be used effectively by dip treating propagation material.

Different races of "F. oxysporum" f. sp. "cubense", Panama disease on banana, can be susceptible, resistant and partially resistant. It can be controlled by breeding for resistance and through eradication and quarantine of the pathogen by improving soil conditions and using clean plant material. Biological control can work using antagonists. Systemic and soil fungicides can also be used.

The main control method for "F. oxysporum" f. sp. "lycopersici", vascular wilt on tomato, is resistance. Other effective control methods are fumigating the infected soil and raising the soil pH to 6.5-7.

The most effective way to control "F. oxysporum" f. sp. "melonis" is to graft a susceptible variety of melon to a resistant root-stock. Resistant cultivars, liming the soil to change soil pH to 6-7, and reducing soil nitrogen levels also help control "F. oxysporum" f. sp. "melonis".

The fungus "Trichoderma viride" is a proven biocontrol agent to control this disease in an environment friendly way.

The amount of initial inoculum will be reduced when a crop other than corn is planted for ≥2 years in that given area; meanwhile proper tillage methods are carried out. Clean plowing and 1-year crop rotation in the absence of corn allows for greater reductions of the disease as well. Note that conventional tilling can reduce disease but can lead to greater soil erosion.

Currently, fungicides and other chemical and biological control agents have proven fairly unsuccessful, or only successful in vitro or in greenhouses, in the face of Panama disease of bananas. The most commonly used practices include mostly sanitation and quarantine practices to prevent the spread of Panama disease out of infected fields. However, the most effective tool against Panama disease is the development of banana trees resistant to "Fusarium oxysporum f. sp. Cubense". Unfortunately, the clonal reproduction of banana has led to a consequential lack of other varieties. Efforts are being made to produce resistant varieties, but with bananas being triploids which do not produce seeds, this is not an easy task. Creating clones from tissue cultures, rather than suckers, has proven somewhat successful in breeding resistant varieties, however these tend to have decreased success in stress-tolerance, yield, or other beneficial traits necessary for commercial varieties. Nevertheless, these efforts are leading to the best control measure for Panama disease of banana.

Recently, an R gene (RGA2) was transformed into Cavendish bananas which confers disease resistance to Fusarium wilt tropical race 4. This is the first case of successful resistance in the field and is a promising step towards preventing the loss of the Cavendish cultivars that are a huge portion of banana export production and subsistence of many communities.

As R.P. Singh, J. Huerta-Espino, and A.P. Roelfs say in their (undated) comprehensive review of literature on the wheat rusts for UN FAO:

"Although Gadd first described stripe rust of wheat in 1777, it was not until 1896 that Eriksson and Henning (1896) showed that stripe rust resulted from a separate pathogen, which they named P. glumarum. In 1953, Hylander et al. (1953) revived the name P. striiformis."

Leaf rust of barley is considered a relatively minor disease in the United States. However, sporadic outbreaks have occurred in the southeastern and Midwestern regions of the country.

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.

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

In Queensland, a farm in Tully, 1500 km north of Brisbane, was quarantined and some plants were destroyed after TR4 was detected on March 3, 2015. After an initial shutdown of the infected farm, truckloads of fruit left in April with harvesting allowed to resume under strict biosecurity arrangements. The government says it is not feasible to eradicate the fungus. Researchers like Wageningen’s Kema say the disease will continue to spread, despite efforts to contain it, as long as susceptible varieties are being grown. The disease was again detected in Tully in July 2017, prompting Biosecurity Queensland to impose quarantine conditions.

Leaf rust is a fungal disease of barley caused by "Puccinia hordei". It is also known as brown rust and it is the most important rust disease on barley.

Banana Freckle is a disease caused by the fungus "Guignardia musae" (telomorph) or "Phyllosticta musarum" (anamorph). Generally, the causal agent of disease is referred to as Guignardia-Phyllosticta sp. There are several different strains of the fungus that exist to infect different banana varieties around the globe. Symptoms include yellowing of the tissue and formation of small dark brown spots on the leaves and fruit. Within the spots, conidia or pycnidia can be found. Banana Freckle is easily propagated and spread from plant to plant by rain splash and movement of infected tissue or fruit. Management of the disease consists of cutting out infected leaves, the paper bag method, fungicide application, and proper sanitation techniques. This devastating disease is extremely relevant for the major banana exporting countries of the world. In the absence of chemical control, there is about a 78% yield loss. Banana Freckle disease needs to be carefully monitored in order to prevent further spread of the disease.

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.

"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%.

This disease is mainly found in tropical climates in Southern Asia, however some scattering exists:

Velvet Blight is a disease that affects the stems, branches, leaves, fruits or trunks of plants and trees. This disease is primarily caused by three fungal species from the genus "Septobasidium": "S. bogoriense", "S. pilosum" and "S. theae".

It is known to affect mainly tea plants ("Thea" genus).

The most studied of these species is "S. bogoriense", most notably due to the work of Ernst Albert Gäumann. "S. bogoriense" is named after the Herbarium Bogoriense (Bogor, West Java, Indonesia) which is the place where it was first identified on the bark of an unspecified tree and named by E. Nyman on June 3, 1898. This species was also listed in Otto Warburg's Monsunia in 1900.

Fusarium wilt is a common vascular wilt fungal disease, exhibiting symptoms similar to Verticillium wilt. The pathogen that causes Fusarium wilt is "Fusarium oxysporum" ("F. oxysporum"). The species is further divided into forma specialis based on host plant.

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.

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.

Prevention of Kashin–Beck disease has a long history. Intervention strategies were mostly based on one of the three major theories of its cause.

Selenium supplementation, with or without additional antioxidant therapy (vitamin E and vitamin C) has been reported to be successful, but in other studies no significant decrease could be shown compared to a control group. Major drawbacks of selenium supplementation are logistic difficulties (daily or weekly intake, drug supply), potential toxicity (in case of less controlled supplementation strategies), associated iodine deficiency (that should be corrected before selenium supplementation to prevent further deterioration of thyroid status) and low compliance. The latter was certainly the case in Tibet, where a selenium supplementation has been implemented from 1987 to 1994 in areas of high endemicity.

With the mycotoxin theory in mind, backing of grains before storage was proposed in Guangxi province, but results are not reported in international literature. Changing from grain source has been reported to be effective in Heilongjiang province and North Korea.

With respect to the role of drinking water, changing of water sources to deep well water has been reported to decrease the X-ray metaphyseal detection rate in different settings.

In general, the effect of preventive measures however remains controversial, due to methodological problems (no randomised controlled trials), lack of documentation or, as discussed above, due to inconsistency of results.