In this study, 37 yeast strains belonging to 19 different species, which had been isolated from various Turkish sugary foods, were characterized by molecular methods. Identification of yeast isolates at the species level was performed with restriction fragment length polymorphism-polymerase chain reaction (RFLP-PCR) by using five different restriction enzymes (MspI, HaeIII, AluI, RsaI, and ScrFI). For each enzyme, different restriction patterns obtained for endogenic yeast strains were compared to those obtained for the control (type or reference) strains. The strains could be identified when their digestion profiles obtained by all of the enzymes matched those of the control strains. Among the yeast strains, 16 could be identified adequately by RFLP-PCR. Tested yeast species were determined as Candida colliculosa, Candida guilliermondii, Candida kefyr, Candida lambica, Candida parapsilosis, Candida pelliculosa, Candida pulcherrima, Pichia anomala, Saccharomyces cerevisiae, Torulaspora delbrueckii and Zygosaccharomyces rouxii. Strain variation was determined by randomly amplified polymorphic DNA (RAPD-PCR) analysis by using (GTG)(3) and M13 primers. The discrimination among the strains were detected by cluster analysis. Generally, strains of the same species clustered together with a few exceptions. By this way, all the strains in the same species could be differentiated by using both the primers.