[Background] Zygomycotan fungi are widely distributed in nature. While some members are harmful, more zygomycotan fungi play an important role in industry, food, medicine, biological control, and so on. They have just been reported sporadically in the Tibet and lack a systematic survey. A large number of potential species need to be isolated, identified, understood, preserved and exploited. [Objective] To understand the species diversity of zygomycotan fungi in the Tibet, and lay a foundation for the control of harmful zygomycotan fungi and the utilization of beneficial ones in this area. [Methods] Zygomycotan fungi isolated with plate dilute method from 701 samples in 19 representative counties all over the seven prefectures of Tibet, were identified morphologically and molecularly, with SSU, ITS and LSU rDNA as markers. Based on these data, the biodiversity, dominant and rare taxa of Tibetan zygomycotan fungi were analyzed. [Results] Tibetan zygomycotan fungi obtained here were classified into 10 genera and 26 species. Among these species, five have been reported in the Tibet, while 21 species are new to Tibet; Four species are even new to China, which are Mortierella amoeboidea, M. globalpina, Mucor brunneogriseus and M. fuscus. The diversity index analysis of Tibetan zygomycotan fungi showed significant differences in the number and composition of species among regions. The most diverse four counties are Bome, Mainling, Dangxung and Baxoi. Analyses of species and genera revealed two dominant zygomycotan genera in the Tibet, Mortierella and Mucor, as well as three dominant species Mortierella alpina, Mucor hiemalis, and Rhizopus stolonifer. Eight common genera are Absidia, Actinomucor, Cunninghamella, Rhizomucor, Rhizopus, Syncephalastrum, Umbelopsis and Zygorhynchus. Common and rare species are 9 and 14, respectively. [Conclusion] The zygomycotan fungi in the Tibet are rich and significantly different in biodiversity among regions. Rare species account for more than half, implying the importance of protecting the natural environment of Tibet.