BACKGROUND: Based on the information no research has been done on the identification and isolation of anaerobic fungi in the Baloochi sheep’s rumen in the dry climate up to now. Objectives: The purpose of this research was the separation and study of the appearance morphology of anaerobic fungi in the Baloochi sheep’s rumen in Sistan region. Methods: The semi-defined medium environment was used in this research for cultivation, separation and purification of anaerobic fungi. Sampling from the solid and liquid contents of 50 Baloochi sheep was done randomly in Zabol slaughterhouse and these samples were used as the source of fungus to inoculation to culture. The roll bottle method was used for purification of rumen fungi. The antibiotic solutions (ampicillin, penicillin, streptomycin, oxytetracycline and chloramphenicol) were used for inhibiting growth of bacteria. Samples of pure fungi were transferred to culture and were observed after growth in glass slide with light microscope. The separated fungi were all monocentric and had rhizoid. Results: With regard to morphologic characteristics the genera of Neocallimastix and Piromyces and species of Piromyces communis, Piromyces minutus, Piromyces rhizinflata, Caecomyces communis was isolated in rumen of Baloochi sheep. Conclusions: With identification of these fungi species in rumen of Baloochi sheep, it is recommended to perform molecular test and enzyme extraction for further survey of characteristics in future research.