© 2014 The Authors. The relative contributions of environmental and spatial processes in macroinvertebrate community structure (i.e., β-diversity) for three functional groups classified on the basis of dispersal ability and microhabitat selection (seagrass-associated [SA], drift-faunal [DF], and benthic-faunal [BF] groups) were examined in a seagrass ecosystem along the Sanriku coast of Japan. Variation partitioning was conducted to explain the environmental heterogeneity and spatial arrangement of local communities (i.e.,degree of variation in the community) for each functional group. Processes determining community structure and metacommunity type differed among the functional groups. The SA group was under greater influence of environmental control, whereas the fractions of β-diversity in the DF and BF groups were explained by only spatial predictors. Thus, even if macroinvertebrate communities live in the same ecosystem, different mechanisms may determine the functional community structure, which depends on ecological traits such as dispersal ability and microhabitat. Ecological processes underlying community assembly differ among functional groups, indicating that the existence and/or dynamics of seagrass patches may affect the variation of faunal functions in an ecosystem.