Natural whey cultures (NWC) (n = 29) used for traditional water-buffalo Mozzarella cheese manufacture and arising from different geographical areas of production were characterized and grouped on the basis of their capability to develop neutral volatile compounds and according to their microbial diversity as revealed by molecular analysis. The flavoring properties of NWC were studied in dairy microcosms resembling the specific technological procedure used in the traditional water-buffalo Mozzarella cheese-making. Neutral volatile compounds were identified by high-resolution gas chromatography (HRGC)-mass spectrometry analysis while information on the microbial diversity occurring in the NWC was retrieved by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of 16S rDNA after direct DNA extraction. Neoformation volatile substances (n = 27) were found; 23 were identified and some of them recognized as odor-conferring molecules. Eight different bands, referable to eight microbial species, were obtained by PCR-DGGE analysis of the NWC. Statistical analyses were applied to PCR-DGGE and HRGC data. Interestingly, the flavoring capabilities and the microbial diversity of the NWC proved to be closely linked and both related to the geographical origin of the NWC. These results suggested a possible use of the molecular characterization of the dairy products to support the traceability criteria of typical dairy products like water-buffalo Mozzarella cheese.