Traditional sourdoughs are considered an important ecosystem where several species of lactic acid bacteria and yeasts cohabit and are responsible for excellent and unique characteristics of the products obtained. In this work, 16 samples of artisanal sourdoughs from tender wheat flour (Triticum aestivum) produced in a southern Italian region (Molise) were studied. The identification of lactic acid bacteria was carried out by traditional methods and genetic techniques (RAPD-PCR). The comparative use of these techniques permitted to identify 84 isolates as Lactobacillus sanfranciscensis (63.1%), Lactobacillus brevis (15.5%), Lactobacillus brevis ssp. lindneri (13.1%), Lactobacillus plantarum (7.1%) and Lactobacillus fermentum (1.2%). Sourdough samples from the different areas of the Molise region showed particular features and different compositions in Lactobacillus species.