Aims: To distinguish Italian Protected Designation of Origin (PDO) water buffalo Mozzarella from different producers on a molecular basis in relation to the place of manufacturing within the production district, and to develop a tool for genetic traceability of typical dairy products. Methods and Results: Microbial DNA was isolated from Mozzarella's governing liquid to amplify the whole microflora's ribosomal 16S-23S internal transcribed spacers (ITS)-PCR fingerprinting by means of an original primer pair. Phylogenetic distance analyses were performed on the obtained electrophoretic band patterns by maximum parsimony and neighbour-joining tree construction algorithms for discrete binary data, using a conventional bootstrap resampling test. The observed band profiles showed high repeatability and specificity, allowing unambiguous distinction of each sample; phylogenetic analyses yielded the same tree topology with good strength of nodal support. Moreover, a relationship between the genetic distances among samples and the actual geographical ones separating the respective producing dairies was observed. Conclusions: The genetic diversity of PDO water buffalo Mozzarella's microflora, observed by ITS-PCR fingerprinting, can be exploited to discriminate cheeses from differently located dairies. Significance and Impact of the Study: Given the increasing importance of food traceability for safety, quality and typicalness issues, the ITS-PCR fingerprinting protocol described here may represent a suitable tool for tracing the geographical origin of Italian Mozzarella.