In natural and engineered ecosystems, diverse species of microbes coexist and interact, resulting in the emergence of community functions. Since microbes have evolved under such circumstances, it is reasonable to deduce that they have acquired strategies for specific interspecies interactions in complex microbial communities. In this review, we discuss the ecological and evolutionary interactions in syntrophic methanogenic consortia comprised of organic acid-oxidizing bacteria and methanogenic archaea. These microbes are known to exhibit mutual interactions (syntrophy), although the molecular mechanisms underlying these sophisticated partnerships have only just been discovered. In addition, recent genomic studies have provided insights into evolutionary interactions among members of methanogenic consortia, from which a novel concept termed "niche-associated evolution" has been proposed for interpreting how specialists evolve in a biological community. We suggest that microbial interspecies interactions are much more complex and sophisticated than hitherto realized and pivotal to the development and functioning of microbial communities.