Abstract Species diversity of Malassezia in the cerumen of nonhuman primates (NHPs) belonging to the Cercopithecidae and Hylobatidae families was investigated. Isolates from cerumen samples collected from carcasses were identified at the species level using 26S rRNA sequence analysis, and intraspecific genetic variation was evaluated using internal transcribed spacer sequences. Fifteen strains were isolated from 30 cerumen samples. They were all identified as Malassezia japonica and clustered into three phylogenetic groups. Malassezia japonica is not a dominant species on human skin, but the results obtained suggest its adaptation to the skin of NHPs.