Abstract:[Background] Lhalu Wetland was the highest and largest urban natural wetland in China. Studying on microbial community structure in Lhalu Wetland could provide theoretical basis for exploitation and protection of biological resources in Qinghai-Tibet plateau, and lay foundation for the study of microbial diversity in wetland ecosystem. [Objective] investigate diversity of mycelial fungus and explore the main environmental factors which influenced the community structure of filamentous fungi in Lhalu Wetland. [Methods] Fungi were isolated from 11 water samples, and identification of fungi were completed using the sequence analysis of nrDNA ITS, combining with traditional classified method. SPSS and CANOCO were used to examine correlations between filamentous fungi diversity and environmental factors. [Results] Mycelial fungi isolated from Lhalu Wetland were belonging to 6 genera and 13 species. Mucor, Cladosporium, Galactomyces were the dominate genera in the wetland. M. hiemalis、M. racemosus and G. geotrichum were the dominate species. Statistical analysis indicated that TN has significantly negative correlation with the counts of filamentous fungi at the Lhalu Wetland (P<0.05), moreover, TN and TP had significant effect on distribution of the fungi, which positively correlated with M. racemosus but passively correlated with M. hiemalis. [Conclusion] Environmental variable has been one of the major factors that influencing wetland microorganism community structure, therefore, it was crucial concerning to study the relationship between environmental factors and diversity of microbe in Tibet.