A total of five strains were isolated from two different hybrid rice seeds samples (Oryza sativa L. Shenliangyou 5814 and Yliangyou 900) in Sanya city, Hainan province, China. Sequence analysis and physiological characteristics indicated that these strains were identical and represented a novel species. Molecular phylogenetic analysis of the D1/D2 domain of the large subunit rRNA gene and the internal transcribed spacer regions revealed that this new species is located in the Microsporomyces clade, with four closely related species, namely, M. magnisporus, M. orientalis, M. bloemfonteinensis, and M. pini. The novel species differed from these four described species in ability to assimilate sorbose, cellobiose, lactose, D-arabinose, and maltose. Based on these results, the following novel yeast species is proposed: Microsporomyces hainanensis sp. nov. with the type strain of Z8(T) (CICC 33066(T) = CBS 14092(T)) belongs to phylum Basidiomycota, subphylum Pucciniomycotina, class Cystobasidiomycetes, family Microsporomycetaceae. The new species were registered in MycoBank under MB 815471.