The human pathogenic yeast genus Malassezia may be an etiological agent of skin disorders and has received considerable attention from dermatologists in recent years. To investigate the different susceptibilities of Malassezia species to four antifungal drugs, we isolated a total of 244 Malassezia strains and identified six species of Malassezia from patients with clinical skin diseases. The minimum inhibitory concentration (MIC) of the four antifungal drugs was obtained by comparing the susceptibility of the isolated Malassezia strains to four antifungal drugs (ketoconazole (KTZ), itraconazole (ITZ), fluconazole (FLC) and amphotericin B (Am B)). We demonstrated that M. furfur, M. sympodialis, M. pachydermatis and M. globosa are the most common Malassezia species in the three skin diseases. The MICs of KTZ, ITZ, FLC and Am B against M. furfur, M. sympodialis, M. pachydermatis and M. globosa ranged from 0.03 - 16 mg/L, 0.03 - 2.0 mg/L, 0.03 - 8 mg/L, and 13 - 64 mg/L, respectively. The sensitivities of Malassezia to the four antifungal drugs from high to low were ITZ ≥ KTZ > Am B > FLC. The susceptibilities of the various Malassezia species to the four antifungal drugs were different, and the susceptibility of M. furfur to KTZ was significantly different from those of the three skin diseases (pityriasis versicolor, Malassezia folliculitis and seborrheic dermatitis). Our results suggested that the MIC analysis of the four antifungal drugs would be helpful in preventing drug resistance in the clinical screening of Malassezia and choosing better antifungal drugs to treat Malassezia-associated skin diseases. © 2020 The Author(s)