[Objective] To obtain the carotenoid-producing yeast with potential application value, 379 strains of yeasts were isolated and screened from Fuxian Lake samples. [Methods] Carotenoids were extracted using acid-heating method, the content of carotenoids was determined by ultraviolet spectrophotometer, and the distribution features of the carotenoid-producing yeasts were analyzed by SPSS software. [Results] 318 yeast strains (83.91% of the tested strains) could produce carotenoids. The yields of carotenoid among most strains ranged from 10 to 300 μg/g, and the highest amount was up to 590.83 μg/g. These strains mainly belonged to the genera Rhodosporidium and Rhodotorula; and the carotenoid-producing abilities of basidiomycetous yeasts were higher than those of ascomycetous yeast strains. In this study, 9 strains with high carotenoid-producing abilities were obtained, namely Rhodosporidium diobovatum (3 strains), Rhodosporidium paludigenum (2 strains), Rhodotorula glutinis, Rhodotorula graminis, Sporidiobolus ruineniae, and Cystofilobasidium macerans (1 strain respectively). [Conclusion] Large numbers of the carotenoid-producing yeasts inhabited Fuxian Lake, and the “red yeasts” were higher yielding yeasts than others. The major groups of carotenoid-producing yeasts were Rhodosporidium and Rhodotorula.