The broadening of fermented milk beverage assortment with probiotic products containing bacteria of Bifidobacterium and Lactobacillus genera prompts to develop reliable and fast methods for the quantitative and qualitative control. The aim of the present study was, therefore, to apply Polymerase Chain Reaction (PCR) carried out on DNA template extracted directly from beverages (a step of strain isolation excepted) for the detection and identification of Lactobacillus and Bifidobacterium cultures to evaluate commercial kefirs and yoghurts. Bacterial DNA was extracted from 3 kefirs and 5 yoghurts of 5 producers. Bacterial species were identified with reference to the type strains using primers specific to the Lactobacillus and Bifidobacterium genera; L. casei group; L. acidophilus, L. delbrueckii subsp. bulgaricus/lactis, L. fermentum, L. johnsonii, L. plantarum, L. rhamnosus, B. animalis/lactis, B. bifidum, B. breve, B. longum species. On the basis of positive PCR results, the presence of Lactobacillus cultures was stated in all yoghurts and kefirs, and that of Bifidobacterium cultures – in those with appropriate declaration. The applied primer sets enabled detection of the species of L. acidophilus, L. casei, L. johnsonii, and B. animalis/lactis in kefirs, and those of L. delbrueckii subsp. bulgaricus, L. casei, L. johnsonii, L. acidophilus, L. fermentum, and B. animalis/lactis in yoghurts. Identification of Lactobacillus species was satisfactory, whereas that of Bifidobacterium species was sporadically unsuccessful, which indicates that the determination of low-number Bifidobacterium cultures demands more efficient DNA extraction and/or more sensitive detection methods to be applied in the fermented milk control.