Background: The purpose of this study was to determine the species distribution and to monitor the antifungal susceptibility profiles of clinical Candida isolates collected in China from 2009 to 2013. Methods: The antifungal susceptibilities of 952 Candida isolates were tested. Results: Candida albicans was the most common species, accounting for 65.7% of the total isolates. The most frequently isolated non-albicans Candida species in this study was Candida glabrata (193, 20.3%). Nearly 7.6%, 3.2%, 1.8%, and 1.1% of the 952 isolates exhibited decreased susceptibility to fluconazole, voriconazole, itraconazole, and flucytosine, respectively. Moreover, seven C. albicans and one Candida krusei had an amphotericin B minimum inhibitory concentration (MIC) of 2 μg/ml. Conclusions: The distribution of species and the prevalence of antifungal resistance in Candida isolates varied among different areas in China. Continuous monitoring of resistance patterns is necessary to control the spread of resistance in clinical isolates of Candida species.