The aim of the study was to evaluate intercluster and intracluster phenotypic and genetic diversity of Leuconostoc spp. PFGE and RAPD-PCR were used to evaluate molecular diversity. Carbohydrate metabolism of the isolates was evaluated using API 50CH. The study demonstrated that genetically closely related isolates will not necessarily demonstrate the same phenotypic relatedness, indicating that phenotypic traits are isolate specific. Therefore, genetic selection of isolates by clustering for further phenotypic characterisation of representatives, might lead to loss of important phenotypic diversity. Furthermore, PFGE was shown to be an efficient molecular tool for the differentiation of Leuconostoc mesenteroides subsp. cremoris and Leuconostoc pseudomesenteroides, that has not been reported previously. Additionally, amygdaline, arbutine, l-arabinose and mannitol can be important fermentation traits for phenotypic differentiation of Ln. mesenteroides subsp. cremoris and Ln. pseudomesenteroides.