A group of eight Gram-positive rods was isolated during a screening of Lactobacillus spp. in dental caries. All strains were isolated on MRS agar and revealed cell and colony morphology typical for the genus Lactobacillus. Phenotypical identification using conventional tests and API 50CH kit assigned all strains as Lactobacillus sp. biochemically close to Lactobacillus brevis. Further investigation using rep-PCR with the (GTG)5 primer separated analysed group into a homogeneous cluster clearly separated from all lactobacilli included in the in-house CCM database but their (GTG)5-PCR fingerprints matched well Streptococcus mutans representatives. Further comparison of biochemical test results with characteristics stated for S. mutans clearly confirmed all strains as members of this species. Our results showed that S. mutans strains retrieved from dental caries can be misidentified as Lactobacillus sp. due to their good growth on MRS agar in typical Lactobacillus-like Gram-positive rods and revealed (GTG)5-PCR fingerprinting as a reliable and fast taxonomic tool for identification of S. mutans. Financial support from projects 1M0528 and MSM0021622416 is gratefully acknowledged.