Phenotypic and genotypic characteristics of lactic acid bacteria were studied to evaluate the microbial diversity of Pecorino Toscano, an Italian cheese with the Designation of Protected Origin, produced from pasteurised sheep milk. Sugar fermentation profiles did not enable unambiguous identification of all the strains, which belonged to Lactococcus lactis subsp. lactis, Streptococcus thermophilus and mesophilic lactobacilli. Numerical analysis of the discriminating phenotypes and PCR fingerprinting showed a high strain heterogeneity. By combining phenotypic and genotypic information, a different distribution between strains was observed. Although produced from pasteurised milk, Pecorino Toscano is characterised by a nide heterogeneity of lactic microflora.