Yogurt is a fermented milk product produced by two homofermentative lactic acid bacteria, Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus. It is consumed throughout the world as a healthy, nutritional food. In this study, the strains of Lactobacillus and Streptococcus were isolated from raw milk samples collected from different local geographical regions of Turkey. One hundred and thirty isolates were characterized to genus level by classical morphological, physiological and biochemical tests. Twenty six of all isolates were identified as L. delbrueckii subsp. bulgaricus and 47 isolates were identified as S. thermophilus using API 50 CHL system. RAPD-PCR was used to explain molecular characterization and genetic differentiation of a total of 73 strains. The whole cell protein profiles of these strains were tested by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). In this study, all strains were identified by the RAPD-PCR technique to species or strain level. SDS-PAGE was also shown to be an effective method for molecular differentiation all of the strains. Phenotypic identification, RAPD-PCR and SDS-PAGE proved to be informative methods suitable to explain molecular characterization and genetic differentiation of L. delbrueckii subsp. bulgaricus and S. thermophilus strains isolated from raw milk. In the present study, we described an identification system by using RAPD-PCR and SDS-PAGE techniques and used this system for genetic differentiation of L. delbrueckii subsp. bulgaricus and S. thermophilus strains isolated from raw milk. It is believed that these two molecular techniques allow researchers to fill the significant gaps present in our understanding of these organisms by providing a comprehensive view potentially involved in industrially relevant phenotypes from different geographical origin.