Common genera of molds include:
• Acremonium
• Alternaria
• Aspergillus
• Cladosporium
• Fusarium
• Mucor
• Penicillium
• Rhizopus
• Stachybotrys
• Trichoderma
• Trichophyton

The Kōji molds are a group of Aspergillus species, notably Aspergillus oryzae, and secondarily A. sojae, that have been cultured in eastern Asia for many centuries. They are used to ferment a soybean and wheat mixture to make soybean paste and soy sauce. Koji molds break down the starch in rice, barley, sweet potatoes, etc., a process called saccharification, in the production of sake, shōchū and other distilled spirits. Koji molds are also used in the preparation of Katsuobushi.

Red rice yeast is a product of the mold Monascus purpureus grown on rice, and is common in Asian diets. The yeast contains several compounds collectively known as monacolins, which are known to inhibit cholesterol synthesis. A study has shown that red rice yeast used as a dietary supplement, combined with fish oil and healthy lifestyle changes, may help reduce "bad" cholesterol as effectively as certain commercial statin drugs. Nonetheless, other work has shown it may not be reliable (perhaps due to non-standardization) and even toxic to liver and kidneys.

Some sausages, such as salami, incorporate starter cultures of molds to improve flavor and reduce bacterial spoilage during curing. Penicillium nalgiovense, for example, may appear as a powdery white coating on some varieties of dry-cured sausage.

Other molds that have been used in food production include:
• Fusarium venenatum – quorn
• Geotrichum candidum – cheese
• Neurospora sitophila – oncom
• Penicillium spp. – various cheeses including Brie and Blue cheese
• Rhizomucor miehei – microbial rennet for making vegetarian and other cheeses
• Rhizopus oligosporus – tempeh
• Rhizopus oryzae – tempeh, jiuqu for jiuniang or precursor for making Chinese rice wine

Alexander Fleming's accidental discovery of the antibiotic penicillin involved a Penicillium mold called Penicillium rubrum (although the species was later established to be Penicillium rubens). Fleming continued to investigate penicillin, showing that it could inhibit various types of bacteria found in infections and other ailments, but he was unable to produce the compound in large enough amounts necessary for production of a medicine. His work was expanded by a team at Oxford University; Clutterbuck, Lovell, and Raistrick, who began to work on the problem in 1931. This team was also unable to produce the pure compound in any large amount, and found that the purification process diminished its effectiveness and negated the anti-bacterial properties it had.

Howard Florey, Ernst Chain, Norman Heatley, Edward Abraham, also all at Oxford, continued the work. They enhanced and developed the concentration technique by using organic solutions rather than water, and created the "Oxford Unit" to measure penicillin concentration within a solution. They managed to purify the solution, increasing its concentration by 45–50 times, but found that a higher concentration was possible. Experiments were conducted and the results published in 1941, though the quantities of penicillin produced were not always high enough for the treatments required. As this was during the Second World War, Florey sought US government involvement. With research teams in the UK and some in the US, industrial-scale production of crystallized penicillin was developed during 1941–1944 by the USDA and by Pfizer.

Several statin cholesterol-lowering drugs (such as lovastatin, from Aspergillus terreus) are derived from molds.

The immunosuppressant drug cyclosporine, used to suppress the rejection of transplanted organs, is derived from the mold Tolypocladium inflatum.