Rivers consist of reaches with variable habitat structures from upstream to downstream. Although longitudinal changes in ecosystem and community characteristics along a river have long been under investigation, linkages between variation in habitat structure and biotic communities remain unclear. Our research focused on identifying longitudinal patterns of community structure in Japanese and Mongolian rivers. While total taxa richness showed no clear trend, lotic (riffle) and lentic (pool) taxa demonstrated contrasting patterns with the former/latter increasing towards upstream/downstream. Longitudinal variations in the lotic and lentic habitat types were also recognized. The trend in taxa richness appears to be associated with changes in the occurrence and availability of lotic and lentic habitats, which are largely controlled by variation in channel gradient. Thus our observation suggests the importance of lotic/lentic (riffle/pool) dichotomy as a fundamental aspect of heterogeneity in habitat and assemblage structures of river systems.