Background: Onychomycosis, the fungal infection of the toenails or fingernails, is caused by three major groups of fungi including dermatophytes, yeasts and non-dermatophyte molds. The objective of the present study was to determine the incidence of onychomycosis and to identify the causative fungi during a one year period in Yazd, Iran. Materials and Methods: From Apr 2013 to Apr 2014 a total of 273 patients with suspected dermatophytosis were included in this study. Nail-clipping specimens of 71 clinically diagnosed cases of onychomycosis were obtained for mycological examination (KOH preparation and fungal culture). Identification of mycelial isolates was based on morphological appearance and microscopic characteristic of the colony. Supplementary methods for identification of dermatophytes were employed. The species of yeasts were identified by germ-tube and chlamydospore test, as well as colony color on chromogenic CHROMagar Candida medium, and the assimilation profile in API 20C Aux system. Results: Of the 71 patients affected by nail disorders, 26 (36.6%) patients of onychomycosis including 54.9% male and 45.1% female (20 fingernails, 6 toenails) via direct examination and/or culture methods were diagnosed. saprophytic fungi were the most prevailing causative agents of onychomycosis and account for up to 69.2%(n=18) of cases, yeasts and dermatophytes were identified as causative agents of onychomycosis in 7 (26.9%) patients and 1 patient (3.8%), respectively. Distribution of fungal isolates was as follows: Aspergillus niger (26.9%), A. fumigatus (19.2%), Candida albicans (15.3%), A. flavus (11.5%), C. tropicalis (7.6%), Penicillium sp. (7.6%), C. dubliniensis (3.8%), Trichophyton mentagrophytes (3.8%) and Fusarium sp. (3.8%). Conclusion: Because of considerable prevalence of onychomycosis, necessity for a careful mycological examination in patients with nail disorders is highlighted.