The analysis of 16S rDNA sequence of bacteria in feces of Hokkaido native horses and light horses were performed to compare the hindgut microbiota between the two breeds. One hundred and four bacterial 16S rDNA clones (57 clones from four native horses and 47 clones from two light horses) were obtained. Only four sequences (3.8% of total sequences) showed 97% or more similarity to known species. The sequences were mainly affiliated with Cytophaga–Flavobacter–Bacteroides and low GC Gram-positive bacteria (LGCGP). Proportion of LGCGP was higher in light horses. Other phyla including Verrucomicrobia, Spirochaetes and Archaea were detected only for native horses, suggesting high diversity of microbiota in native horses. In LGCGP, clusters related to known cellulolytic species were found only for native horses, while a cluster related to soluble sugar-utilizing species was detected only for light horses. The library composition-comparing software LIBSHUFF showed significant (P < 0.05) difference of fecal microbiota between the horse breeds. The number of Fibrobacter succinogenes-related sequence and the frequency of detection of novel groups were found to be higher in native horses by selective amplification analysis. The results suggest that genetic diversity and population size of the F. succinogenes group are higher in the hindgut of native horses.