Raw milk from Sardinian cows and sheep, and sheep's milk yoghurt (Gioddu), are food products that are poorly characterized in terms of the presence of mesophilic Lactobacillus strains, and may be good sources from which to isolate novel bacterial strains. Sixteen Lactobacillus strains were identified by genotypic and phenotypic methods from samples of sheep's milk ( n =7), fermented sheep's milk ( n =7) and one sample of cows’ milk. These strains were further characterized for the presence of functional traits useful for probiotic applications, such as resistance to simulated gastric acid, resistance to bile salts, and adhesion of two different cell lines (Caco-2 and MIM/PPK). Moreover, selected aspects correlated with safety (antimicrobial susceptibility and presence of plasmids) and ecological roles (ability to produce biofilms and bacteriocin-like substances) were tested. All but 1 of the 16 strains were unambiguously allotted to three species, L. paracasei (5 strains), L. plantarum (8 strains), and L. reuteri (2 strains). Many of the strains exhibited characteristics suggesting that they would survive in the gastrointestinal tract and also had the capability to attach to various cells. Greater variability was observed for the other traits analyzed. These data suggest that Sardinian artisan dairy products are interesting sources for the isolation of bacterial strains with characteristic and differentiated functional traits.