Ninety-two yeast strains causing spoilage on different kinds of Turkish white cheeses were isolated and identified on the basis of their physiological and morphological properties. The identified isolates represented 12 species belonging to 8 genera. The most prevalent isolates belonged to the species Debaryomyces hansenii (32.6%), Kluyveromyces marxianus (18.5%) and Yarrowia lipolytica (17.4%). Other genera encountered were Pichia, Torulaspora, Candida, Williopsis, and Galactomyces. They were genotypically characterized with PCR amplification of the species-specific internally transcribed spacer (ITS) of 5.8S ribosomal DNA (ITS-PCR). ITS-PCR of 15 strains of Y. lipolytica, 15 strains of K. marxianus and 25 strains of D. hansenii resulted in single fragments of 360, 740 and 640 bp, respectively. Proteolytic and lipolytic activity within yeast strains isolated from cheese was observed. Lipolytic and proteolytic organisms play an important role in the maturation of cheese and in the spoilage of dairy products. Usage of identification systems based on biochemical and physiological characteristics takes longer time and often results in misidentifications. In this study, false identification of 5 strains of D. hansenii, 2 strains of K. marxianus, 1 strain of Y. lipolytica, 1 strain of Torulaspora delbrueckii, 1 strain of Pichia anamola and 1 strain of Candida sake by using conventional methods confirmed the mentioned statement above. As a consequence, ITS-PCR was found to be more rapid, reliable, easy to perform and cost effective than biochemical approaches.