[Background] 16S rRNA gene sequence is widely used in the classification and identification of bacteria, although still with some limitations. The housekeeping gene as a molecular marker has its unique advantages in phylogenetic analysis among related species and subspecies. [Objective] We used 16S rRNA, uvrC (excinuclease ABC subunit C) and murE (UDP-N-acetylmuramyl tripeptide synthase) gene sequences to identify the phylogenetic relationship among Lactobacillus casei and its related species/subspecies. [Methods] six L. casei strains isolated from traditional dairy products were selected. The uvrC and murE gene sequences of each isolates were obtained by polymerase chain reaction (PCR) methods and sequencing technology. Then, we estimated the genetic distance and constructed phylogenetic trees of 6 L. casei strains combined with 5 published related species/subspecies based on the sequences of 16S rRNA gene, uvrC and murE gene, respectively. [Results] Phylogenetic trees indicated that the homology of closely related L. casei species among uvrC, murE, the combined genes (uvrC-murE) and 16S rRNA gene were different, ranged from 79.00% to 99.16%, 89.08% to 99.20%, 76.56% to 99.69% and 99.58% to 100%. L. casei and its related species and subspecies cannot be distinguished by 16S rRNA gene sequence analysis. The phylogenetic tree based on the sequences of combined gene (uvrC-murE) had a distinct classification on genetic relationship of L. casei and its related species and subspecies. [Conclusion] Phylogenetic analysis based on the combined gene (uvrC-murE) can be used as a supplementary of 16S rRNA gene analysis for rapid classification and identification of L. casei and its related species and subspecies.