The incidence of fungal infections has increased in recent years. Antifungal resistance is a major problem with increasing frequency due to the widespread use of antifungal agents in infections. Identification of the Candida species and susceptibility patterns with the appropriate tests for resistance and selection of the empirical agents used for treatment are important. The aim of the study was to evaluate the changes of the epidemiology of Candida species and minimum inhibitory concentrations (MIC) of the antifungal agents, isolated in Mycology Laboratory of Ondokuz Mayıs University Faculty of Medicine, between 1 January 2009 to 1 July 2012. The study was performed retrospectively based on records in the mycology unit and checked comparatively with the automation system in the hospital. The recurrent reproductions of the same patient were excluded. For the identification of Candida species API®ID 32C (bioMerieux, France) system was used. Information on the isolated material, patient's age, gender and the inpatients' clinics were recorded. The susceptibility of Candida species isolated from blood cultures were studied with Etest (bioMerieux, France) method. A total of 1238 isolates were included in the study. The most common species isolated from clinical samples was C.albicans with a rate of 51.1% (n= 632), followed by C.tropicalis with a rate of 15.8% (n= 195). Among the pediatric intensive care unit (ICU) patients C.parapsilosis 42% (n= 17) was the most common isolate and the second most common isolate was C.albicans 32% (n= 13). However, in the adult ICU the most common isolate was C.albicans 34% (n= 13) and the second was C.parapsilosis 31% (n= 12). When the distribution of Candida species were analyzed from the records of last four years, the frequency rate of C.albicans and non-albicans species was found as 51.1% (n= 632) and %48.9 (n= 606), respectively. Based on these data, a comparison was made between the years and no difference between the two groups in terms of the distribution of fungi within the specified time (x²: 3.2, df: 1, p: 0.073) was determined. Of the Candida species isolated from blood cultures, seven isolates (2.2%) were resistant to fluconazole in the study period. The differences of MIC levels in fluconazole were detected between the years 2010-2012 and 2011-2012. The geometric mean of the MICs in 2012 increased significantly compared to 2010 and 2011 (p 0.05). According to the sensitivity results, fluconazole is still seen as an option that can be used for the first choice. Although it remains as the first antifungal choice, antifungal susceptibility testing of the identified fungi will help the clinician for the plan and continuation of the treatment.