Meat fermentation and fermented sausage manufacturing are ancient processes in Europe, and typical preparations based on fermentations driven by indigenous microflora are still produced by local meat factories or artisanal producers without the use of starter cultures (Rantsiou et al., 2005a; Urso et al., 2006). LAB (Lactic Acid Bacteria) and CNC (Coagulase Negative Cocci) are the two main groups of bacteria with technological value determining the several biochemical and physical reactions taking place during the fermentation and ripening of sausages (Rantsiou & Cocolin 2006). Interest in preserving the biodiversity of microorganisms involved in the fermentation of food products has been reported (EC 1999; Aymerich et al., 2006). As a consequence, and also taking into consideration the technological and economic importance of these microorganisms, the availability of methodologies able to unequivocally characterise single species, potentially right up to strain level, is called for. Identification of species, particularly within the genus Lactobacillus, using phenotypic methods such as sugar fermentation or other biochemical traits, may produce ambiguous results and be complicated because of the presence of several LAB species with similar characteristics (Quere et al., 1997). Molecular methods are nowadays increasingly employed to clarify the taxonomy of microbiota from sausages. The largest number of works is based on RAPD (Random Amplified Polymorphic DNA), (Rebecchi et al., 1998; Rantsiou et al., 2005a), 16S rDNA sequencing (Rantsiou et al., 2005a), PCR-DGGE (Denaturing Gradient Gel Electrophoresis) analysis (Cocolin et al., 2001a; Cocolin et al., 2001b; Comi et al., 2005; Urso et al., 2006), and REA-PFGE (Restriction Endonucleases Analysis Pulsed Field Gel Electrophoresis) analysis (Psoni et al., 2006). The above DNA-based methodologies, with the exception of REA-PFGE, are easy, fast, and provide an accurate identification at species level, but are not as informative when it comes to characterisation of the bacterial population at strain level. Random amplification of polymorphic DNA is useful for performing identification at strain level, but the lack of reproducibility and the lack of complex band patterns, are the main limiting factors. Restriction endonucleases analysis and pulse field gel electrophoresis is a powerful method