Isolation of bacteria from a given environment may cause multiple isolation of the same strain. Verification of such strains is difficult using traditional microbiological methods due to their low discriminative power. Therefore, the PFGE method (Pulsed Field Gel Electrophoresis) as well as Sma I, Apa I and Not I endonucleases were used. Twelve Lactobacillus isolates derived from dairy products and 4 reference strains belonging to species of L. acidophilus, L. casei, L. delbrueckii subsp. bulgaricus and L. helveticus were differentiated. Using Sma I and Apa I enzymes, 14 unique restriction patterns were obtained, and identical genotypes were observed for L. acidophilus 145 and L. acidophilus A isolates (derived from dairy cultures) and for L. acidophilus La5 and L. acidophilus DSM 20079 (from acidophilic milk and human, respectively). Using Not I enzyme, only 12 distinct restriction patterns were obtained. Four strains: L. acidophilus DSM 20079, L. acidophilus La5, L. acidophilus Bs and L. acidophilus K1 were not able to be distinguished with Not I, although they demonstrated different patterns after Sma I and Apa I digestion. In the group of 12 isolates examined, 10 original strains were affirmed. Sma I and Apa I enzymes were characterised by the highest discriminative power. The obtained results confirmed diversity of the strains used in dairy production.