Objective To investigate the distribution of onychomycosis pathogens and susceptibility of pathogens to commonly used antifungal agents in Hainan Province. Methods Nail scrap specimens of patients with onychomycosis in a hospital from May 2016 to November 2018 were collected, isolated fungal strains were analyzed by culture, identification and in vitro antifungal susceptibility testing. Results A total of 348 patients with onychomycosis were collected, 351 strains of pathogens were isolated. The main pathogens were yeast-like fungi (53.28%), dominantly Candida parapsilosis (22.22%) and Candida albicans (11.40%), followed by Dermatophytes (29.63%), dominantly Trichophyton rubrum (25.07%). Fungal strains were mainly isolated from patients in age groups of 21-30 years old (86 strains), 31-40 years old (77 strains) and 41-50 years old (49 strains); the ratio of male to female patients was 1:1.52. The main clinical types of onychomycosis were distal lateral subungual onychomycosis (47.41%), superficial white onychomycosis(18.97%), and total dystrophic onychomycosis(15.80%). Geometric mean of MIC of Trichophyton rubrum and Trichophyton interdigitale to terbinafine was the lowest, geometric mean of MIC of Fusarium solani to vriconazole was the lowest, geometric mean of MIC of Candida (Candida albicans, Candida parapsilosis, Candida tropicalis, and Candida dubliniensis) to ketoconazole, itraconazole, and vriconazole were all low. Conclusion The main pathogen of onychomycosis in Hainan Province from 2016 to 2018 are yeast-like fungi, ketoconazole, itraconazole and voriconazole are preferred for treatment of onychomycosis.