[Objective] To study the population diversity, spatial distribution characteristics, and correlations with physicochemical factors of yeasts in the Napahai plateau wetland. [Methods] Yeast strains were isolated from the water samples of the Napahai plateau wetland by membrane filtration and plate culture. The strains were identified based on the D1/D2 sequences of the 26S rRNA gene and morphological characteristics. R 4.2.2 and Canoco 5 were used to analyze the yeast diversity and its correlations with physicochemical factors. [Results] A total of 565 yeast strains were isolated from the water bodies in the Napahai plateau wetland and identified as 36 species of 21 genera. The dominant species were Rhodotorula mucilaginosa, Meyerozyma guilliermondii, and Rhodotorula graminis. Total nitrogen was the main physicochemical factor affecting the yeast count, which presented a negative correlation. [Conclusion] The water bodies of Napahai plateau wetland harbor abundant yeast resources which present significant spatial heterogeneity. Human activities and total nitrogen have significant impacts on the yeast count. The yeast community composition in the water bodies of the Napahai plateau wetland is significantly different from that in other plateau freshwater lakes and has unique yeast resources that require further research.