Centenarians constitute a significant subpopulation in the Bama County of Guangxi province in China. The beneficial effects of intestinal microbiota, especially bifidobacteria of centenarians, have been widely accepted; however, knowledge about Bifidobacterium species in centenarians is not adequate. The aim of this study was to investigate the quantity and prevalence of fecal Bifidobacterium in healthy longevous individuals. Fecal samples from eight centenarians from Bama (aged 100 to 108 years), eight younger elderlies from Bama (aged 80 to 99 years), and eight younger elderlies from Nanning (aged 80 to 99 years) were analyzed using denaturing gradient gel electrophoresis, species-specific clone library, and quantitative polymerase chain reaction technology (qPCR). A total of eight different Bifidobacterium species were detected. B. dentium, B. longum, B. thermophilum, B. pseudocatenulatum/B. catenulatum, and B. adolescentis were common in fecal of centenarians and young elderly. B. minimum, B. saecularmay/B. pullorum/B. gallinarum, and B. mongoliense were found in centenarians but were absent in the younger elderlies. In addition, Bifidobacterium species found in centenarians were different from those found in Bama young elderly and Nanning young elderly, and the principal differences were the significant increase in the population of B. longum (P < 0.05) and B. dentium (P < 0.05) and the reduction in the frequency of B. adolescentis (P < 0.05), respectively. Centenarians tend to have more complex fecal Bifidobacterium species than young elderlies from different regions.