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Lactic acid bacteria (LAB) play an important role in food fermentation, as the products obtained with their aid are characterized by hygienic safety, storage stability and attractive sensory properties. A major aim of the research in this field is the selection of LAB strains that could be used. Hence it is very important to be able to apply a reliable method to distinguish a particular strain specifically and unambiguously, which allows studies of population dynamics of mixed cultures and monitoring starter strains during fermentation (Ramos & Harlander, 1990).Molecular methods are a powerful alternative to the traditional differentiation of bacteria. A highly reproducible method for characterizing and distinguishing closely related strains, is represented by REA-PFGE (restriction endonuclease analysis by pulsed-field gel electrophoresis) performed by infrequently cutting endonucleases. Genetic differentiation of strains in several species of LAB has been successfully performed by this technique (Moschetti et al. 1997; Villani et al. 1997) obtaining very clear and reproducible restriction patterns (Moschetti et al. 1998).In this study selected inoculated strains (lactococci or lactobacilli) were monitored by REA-PFGE during the whole process of water-buffalo ‘cacioricotta’ cheese-making. This product is a typical and traditional cheese in southern Italy produced from cow, goat, ewe or water-buffalo milk. The original technology of this preparation permits the recovery of whey proteins due to the high heat treatment of whole milk employed, allowing interesting yields to be achieved in terms of cheese. The use of starters is not common in traditional technology but low acid protection of the final product suggested the use of LAB as starter (Emaldi et al. 1987).