In this study, our purpose was to molecular characterize Lactobacillus strains isolated from naturally fermented sausages, produced in three different processing plants in continental Greece, in order to investigate the differences of strains coming from different producing areas. Three-hundred and thirty eight strains were isolated throughout the fermentation periods on MRS. They were identified by species-specific PCR and sequencing of partial 16S rRNA gene. The results obtained highlighted that the main populations involved in the fermentations studied belonged to the species Lactobacillus sakei, Lactobacillus plantarum and Lactobacillus curvatus. However, for each of the fermentations, the percentage of isolation for the three main species was different. Molecular characterization of these strains was performed by RAPD-PCR with primer M13 and cluster analysis was applied to define relations and degrees of similarities between strains. This analysis led to the understanding that some strains were plant-specific, whereas others shared a degree of homology independently of the provenience. This evidence is highlighting the capability of the strains to adapt to specific production condition, becoming the main responsible for the transformations, thereby influencing the final characteristics of the sausages.