Little has been known about symbiotic relationships and host specificity for symbionts in the human gut microbiome so far. are a paragon of the symbiotic bacteria biota in the human gut. In this study, we characterized the population genetic structure of three bifidobacteria species from 58 healthy mother-infant pairs of three ethnic groups in China, geographically isolated, by Rep-PCR, multi-locus sequence analysis (MLSA), and carbohydrate utilization. One hundred strains tested were incorporated into 50 sequence types (STs), of which 29 STs, 17 STs, and 4 STs belong to subsp. , , and subsp. , respectively. The conspecific strains from the same mother-child pair were genetically very similar, supporting the vertical transmission of phylotypes from mother to offspring. In particular, results based on allele profiles and phylogeny showed that subsp. and exhibited considerable intraspecies genetic heterogeneity across three ethnic groups, and strains were clustered into ethnicity-specific lineages. Yet almost all strains of subsp. were incorporated into the same phylogenetic clade, regardless of ethnic origin. Our findings support the hypothesis of co-evolution between human gut symbionts and their respective populations, which is closely linked to the lifestyle of specific bacterial lineages. Hence, the natural and evolutionary history of species would be an additional consideration when selecting bifidobacterial strains for industrial and therapeutic applications.