Anaerobic chytridiomycete fungi are found in the gastrointestinal tracts of sheep, cattle and goats, as well as in many other domesticated ruminant and nonruminant herbivores and a wide variety of wild herbivorous mammals. They are principally found associated with the fibrous plant particles of digesta and as free swimming zoospores in the fluid phase. The presence of large fungal populations in animals consuming mature pasture or diets largely composed of hay or straw together with the production of highly active fibre degrading enzymes lead to the belief that anaerobic fungi may have a significant role to play in the assimilation of fibrous feeds by ruminants. This paper is focused on anaerobic fungi because of their unusual biology and metabolism, and the biotechnological potential of their cellulases. This book is the first report of anaerobic fungi which were isolated from animals from Macedonia.