Beneficial bacteria in the gut affect human health, and it is generally believed that the assemblage of healthy gut flora is achieved through vertical transmission of by breastfeeding in early infancy. There is limited evidence for the difference in the composition of beneficial bacteria across different mother-infant cohorts and the presence of population-specific microbial taxa. [Objective] To investigate Lactobacillus spp. and the vertical transmission and genetic differences of the dominant species Lacticaseibacillus paracasei among mother-infant cohorts of different ethnic groups, providing a theoretical basis for developing personalized probiotic regimens. [Methods] Lactobacillus strains were isolated from 39 mother-infant pairs of three ethnic groups without mixed marriage in China and identified by repetitive extragenic palindromic PCR (rep-PCR) and groEL sequences. The genetic differences of 83 strains of L. paracasei, a representative species, were analyzed by multilocus sequence typing (MLST). [Results] The species and abundance of Lactobacillus varied among the mother-infant pairs of different ethnic groups. A total of 945 Lactobacillus strains were isolated, belonging to 15 species of 4 genera. L. rhamnosus (20.07%), L. paracasei (16.54%), and L. casei (11.90%) were dominant species in the Han ethnic group, while L. casei (13.55%), L. paracasei (12.69%), and Ligilactobacillus salivarius (11.47%) were dominant bacteria in Uighur ethnic group in Hotan. The dominant species in the Li ethnic group in Hainan were Limosilactobacillus oris (24.55%), L. paracasei (15.85%), and Lactobacillus gasseri (10.87%). The 83 strains of L. paracasei were classified into 11 phylogenetic groups by rep-PCR and 31 sequence types (STs) by MLST, demonstrating ethnic specificity. L. paracasei isolates from the same mother-infant pair had the same STs, and isolates from the mother-infant pairs of the same ethnic group had higher genetic similarity. [Conclusion] Lactobacillus species varied in the mother-infant pairs of different ethnic groups, and L. paracasei strains from the same origin displayed higher genetic similarity, which supported vertical transmission at strain level and ethnic specificity.