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Mesophilic starter cultures used in dairy industry have been traditionally characterised by metabolic and biochemical methods. As closely related species of lactic acid bacteria have often only minor differences in phenotypic traits, which may also be variable within certain species, clear identification is often complicated. Therefore, techniques of molecular biology have been applied for rapid detection and differentiation of lactic acid bacteria. In this work, some bacterial clones isolated from mesophilic starters, which were preliminary identified as lactococci by phenotypic methods, were found to be Leuconostoc strains by both PCR and PFGE. According to the results, genotypic differentiation methods used in combination with phenotypic tests provide a fast and convenient way to reliably identify lactic acid bacteria displaying atypical metabolic characteristics.