The aim of the study was to identify and differentiate five strains isolated from fermented dairy products using species-specific polymerase chain reaction (PCR) as well as PCR of internal transcribed spacer (ITS-PCR) and pulsed field gel electrophoresis (PFGE) in reference to type strains. Results of species-specific PCRs showed that three strains belonged to the species of L. helveticus and two strains to the species of L. casei. Results obtained with both IST-PCR and PFGE method showed low diversity of the isolates since only three different ITS-PCR and PFGE profiles were obtained. Moreover, differentiation conducted merely with PFGE method allowed distinguishing the type L. casei DSMZ20011, L. rhamnosus DSMZ20021 and subsp. paL. paracasei racasei DSMZ5622 strains. Results of this study confirmed that, although time-consuming and expensive, the PFGE method is characterised by the highest discriminatory power in strain differentiation. The ITS-PCR method even though fast, easy and relatively inexpensive, showed to be more suitable for the pre-selection of strains.