Strains ofBifidobacterium longum, Bifidobacterium breve, andBifidobacterium animalisare widely used as probiotics in the food industry. Although numerous studies have revealed the properties and functionality of these strains, it is uncertain whether these characteristics are species common or strain specific. To address this issue, we performed a comparative genomic analysis of 49 strains belonging to these three bifidobacterial species to describe their genetic diversity and to evaluate species-level differences. There were 166 common clusters between strains ofB. breveandB. longum, whereas there were nine common clusters between strains ofB. animalisandB. longumand four common clusters between strains ofB. animalisandB. breve. Further analysis focused on carbohydrate metabolism revealed the existence of certain strain-dependent genes, such as those encoding enzymes for host glycan utilisation or certain membrane transporters, and many genes commonly distributed at the species level, as was previously reported in studies with limited strains. AsB. longumandB. breveare human-residential bifidobacteria (HRB), whereasB. animalisis a non-HRB species, several of the differences in these species’ gene distributions might be the result of their adaptations to the nutrient environment. This information may aid both in selecting probiotic candidates and in understanding their potential function as probiotics.