Rumen is an area with high potential for growing of diverse living organisms including anaerobic fungi. The most studies on rumen fungi focused on anaerobic fungi classified as Chytridiomycetes, family Neocallimasticaceas, while few studies have done on determination of Zygomycetes that can be native in the rumen. The most fungi within the subkingdom Zygomycotina belong to the class Zygomycetes. Fungi in this class possess some distinctive properties that contain rapid growth, nonseptate mycelium, reproduction by sporangiospores (Pitt et al., 1985) and production of some hydrolytic enzymes (Vinogradova et al.,2003). The aim of this study was microscopic examination and molecular analysis of nuclear small subunit (SSU; 18S rDNA) of ruminal fungi, Zygomycete, and its reproductive manner in sheep.