Four hundred strains isolated from Tunisian sheep and goat raw milks were initially screened for their ability to survive the GastroIntestinal Tract (GIT). Forty-three among the four hundred bacteria were resistant to pepsin, pH 2, pancreatin and bile salts at 0.3%, even after 5 hours of incubation. Identification using 16S rRNA gene sequencing was established and we obtained as a species Lactobacillus plantarum (29 isolates from sheep milk and 11 from goat milk) and Lactobacillus pentosus (2 isolates from sheep milk and 1 from goat milk). We showed the ability for auto-aggregation and/or hydrophobicity properties. Finally, both M63 and C78 strains showed an important level of adhesion to three intestinal epithelial cells Caco-2 TC7, HT29-MTX, and HT29-CL.16E. Taken together, these properties allow the lactobacilli strains to be considered promising beneficial strains for developing functional foods for consumers.