Specific bacteria cultures, known as starters, are used for manufacturing of fermented milk products. Yoghurt is made from milk by the protocooperative action of well known starters, namely Lactobacillus delbrueckii ssp. bulgaricus and Streptococcus thermophilus. They lead to coagulation of milk by lactic acid fermentation and other products give the characteristic properties, such as acidity, aroma, and consistency. Traditional method, using part of a previous batch to inoculate a new batch, have been used for centuries. Such cultures lead to variable performance, however industrial production needs consistency. The method of choice is the use of bacterial strains with known physiological, biochemical and genotypic characters. The isolation and identification of natural starters is a need not only for the dairy industry, which still import starters abroad, but also for the preservation of natural lactic acid bacteria diversity of Anatolia. With this perspective, the aim of our study was the isolation of starters from artisanal yoghurts, and their biochemical and molecular characterization. At the end of the study, 66 cocci and 71 bacilli were isolated. According to biochemical identification, all the bacilli isolates were found to be L. delbrueckii ssp. bulgaricus, however cocci isolates showed highly variable sugar fermentation results and only 7 of them were characterized as S. thermophilus. The molecular characterization was based on the amplification and restriction fragment length polymorphism (RFLP) of 16S ribosomal DNA (rDNA) and internal transcribed spacer (ITS) region. Species-specific PCR amplification and 16S sequencing were also used for justification. All of the isolates were well identified with the help of molecular techniques.