Libraries of rumen bacterial 16S rRNA gene sequences of Gayals (Bos frontalis) and Swamp buffaloes (Bubalus bubalis) were cloned and sequenced in the present work to compare the bacterial diversity with the third published library of Holstein cow. Sequence similarity of 97% was used as the definition of operational taxonomic unit (OTU). The majority of the 470 sequences retrieved fell into the phyla of low G + C subdivision (329 sequences) and Cytophaga-Flexibacter-Bacteroides (CFB, 123 sequences) with the percentages of 70 and 26.2, respectively. The remaining clones belonged to the phyla of Proteobacter, high G + C gram positive bacteria (HGCGPB) and Spirochaetes, accounting for 3.8% totally. Only 73 clones (25 OTUs, 15.5%) could be closely related to cultured representatives. However, a larger fraction was related to uncultured representatives. Holstein cow may have more representatives of cultural bacteria and there were more uncultured clones for Gayals. The percentage of cultural representatives was 24, 13.3 and 9.5 for Holstein cow, Swamp buffaloes and Gayals, respectively. Twenty-three OTUs of the 236 ones appeared in more than one library, five of which were cultural. Selenomonas ruminantium, Ruminococcus flavefaciens and Butyrivibrio fibrisolvens were found in two different libraries, while Succiniclasticum ruminis and Pseudobutyrivibrio ruminis were found in all three libraries. Some of the animal-specific bacteria that had not been described previously in the ruminal ecosystem, e.g. Allisonella histaminiformans for Gayals and Staphylococcus sciuri for Swamp buffaloes were also recovered.