Background Archaea belong to the domain Euryarchaeota, represents only 3-5% of the rumen microbiota; however, they play a central role in maintaining the H2 pressure. Host species in conjunction with geographical regions may lead to the variable distribution of rumen methanogens. Indian cattle and buffaloes represent 13 and 53% of the global population, respectively. However, the influence of host species (bovine) and geographical regions on the methanogens distribution has not been investigated in Indian subcontinent. Therefore, the present study was undertaken to explore the rumen methanogens diversity in the cattle and buffaloes native to the two distinct geographical regions of India. Results Next generation sequencing of 16S rRNA gene from 36 rumen fluid samples corresponding to cattle and buffaloes revealed that Methanobrevibacter (Mbr.) genus constituted largest fraction (55-62%) of the rumen archaeal community. Furthermore, Methanobrevibacter gottschalkii was the most prominent methanogens with the significantly higher abundance in cattle. Methanomassiliicoccales represented <10% of the total archaeal community and was found to be the most variable between these two host species. In north region, the distribution of Methanomassiliicoccales, such as Methanosphaera sp., Group 4, Group 8, Group 12 sp. and Group 9 sp. was significantly higher in cattle. The distribution of prominent methanogens, such as Mbr. gottschalkii and Mbr. ruminantium did not differ between two host species in the north region. However, Mbr. gottschalkii was significantly higher in buffaloes as compared to cattle in south region. Mbr. wolinii was exclusively detected in the cattle. Inter-region comparison established that Methanomassiliicoccales were the most variable between the two regions. Conclusions Host species did not affect the distribution of hydrogenotrophic methanogens except for Mbr. gottschalkii. Methylotrophic methanogens, in spite of their limited representation, were most influenced by the host species and geographical regions. Overall, the Methanomassiliicoccales distribution was higher in cattle, and the environmental conditions in north region were conducive for their higher distribution. The variable distribution of methanogens indicated that host and geographical region oriented strategies needs to be developed for the reduction of enteric methane emission. Further studies are warranted to explore the impact of diet on the distribution of rumen methanogens between the host species within and across different environmental conditions.