The numbers of bifidobacteria in fecal samples were specifically determined by colony hybridization with the mixture of digoxigenin-labeled DNA probes that were prepared from whole chromosomal DNA of Bifidobacterium longum 6001 and Bifidobacterium adolescentis 6003. These DNA probes strongly hybridized with DNA of B. longum, B. adolescentis, Bifidobacterium breve, Bifidobacterium suis, Bifidobacterium infantis, Bifidobacterium bifidum, Bifidobacterium angulatum, and Bifidobacterium animalis. Detectable positive signals with DNA of Bifidobacterium pseudolongum ssp. pseudolongum, Bifidobacterium catenulatum, and Bifidobacterium thermophilum were also found after hybridization. When dot-blot hybridization was performed with whole cells of 47 reference strains containing 11 species (16 strains) of bifidobacteria, all of the bifidobacteria tested could be specifically detected by using these DNA probes; Lactobacillus fermentum JCM 1173, however, showed a slight nonspecific signal. The counts of bifidobacteria by colony hybridization in the fecal samples of four of the five subjects were the same as the counts that were obtained by the conventional method using BL agar medium. Furthermore, no significant difference existed in the number of bifidobacteria that were determined by either method.