Lactobacillus is naturally abundant in raw milk. Lactobacilli may develop antibiotic resistance as a result of unconscious antibiotic usage in animals. The aim of this study was to identify Lactobacillus species from raw goat’s and cow’s milk, investigate phylogenetic relationships, and examine the antibiotic profiles of these strains. In this study, the milk of 10 cows and 5 goats was obtained from some farms in Adana. The Crystal method was used to phenotypically identify different colonies assumed to be Lactobacillus that were cultured in milk samples. The disc diffusion test was used to determine their resistance to antibiotics. By using the PFGE method, the phylogenetic relationships of Lactobacillus strains were examined. A total of 18 Lactobacillus strains were isolated from 10 different cows’ milk and 10 Lactobacillus strains were identified from 5 distinct goats’ milk. When the antibiotic susceptibility profiles of the Lactobacillus strains isolated from cow’s milk were examined, it was found that all strains were sensitive to vancomycin and chloramphenicol, and 38.9% of them were resistant to some antibiotics. All the Lactobacillus strains isolated from goat’s milk were shown to be susceptible to ampicillin, vancomycin, chloramphenicol, and 40% of all strains were found to be resistant to some antibiotics. The PFGE analysis showed that 28 Lactobacillus strains were separated into 21 pulsetypes, and the strains in the A-B-C-D-E-F-G pulsetypes were found to be 100% similar. Consequently, the sensitivity of Lactobacillus species to antibiotics requires more investigation.