In this study, 49 yeast isolates, which had been isolated during spontaneous wine fermentation of Kalecik Karasi and Emir grapes, were identified by molecular methods. Nineteen of the 24 Kalecik Karasi isolates and 22 of the 25 Emir isolates could be identified to species level by Restriction Fragment Length Polymorphism (RFLP) of the ITS-18S rRNA gene. The identified Kalecik Karasi isolates were found to be strains of Candida pulcherrima, Candida robusta, Cryptococcus albidus, Kloeckera apiculata, Kloeckera apis, Saccharomyces cerevisiae and Torulaspora delbrueckii. The Emir isolates belonged to Candida krusei, C. pulcherrima, K. apiculata and S. cerevisiae. All of the S. cerevisiae strains and most of the non-Saccharomyces strains could be differentiated by randomly amplified polymorphic DNA (RAPD-PCR) analysis. Although satisfactory results were obtained by M13 primer, (GTG)(3) primer was much more effective in the discrimination of K. apiculata, Cry. albidus and C. krusei strains.