Abstract Although the influence of seagrasses on the diversity and abundance of associated fauna is generally well understood, the effects of seagrass specific identity are not. To determine whether benthic epifaunal and infaunal assemblage patterns vary by the identity of dominant seagrass species in shallow water meadows, we compared quantitative measures of faunal species richness, abundance, and assemblage structure among beds dominated by Cymodocea rotundata, Enhalus acoroides, and Thalassia hemprichii; the study site was at Lopez Jaena, Misamis Occidental Province in the southern Philippines. The Cymodocea-dominated vegetation had higher seagrass shoot density and lower seagrass biomass than those dominated by Enhalus and Thalassia. Across vegetation types, we encountered 30 and 15 species of epifauna and infauna at average densities of 1.73 and 0.82 animals/core (0.0314m2), respectively. Neither densities and species richnesses of epifauna and infauna nor species composition varied significantly by vegetation type. Multivariate analyses of macrofaunal assemblage structure and abiotic/biotic environmental factors demonstrated that seagrass aboveground biomass explained a significant proportion of the multivariate variation in epifaunal species composition (39%); none of the potential explanatory variables was related to variation in ecological parameters of the infauna. Thus, seagrass specific identity is not a good predictor of either macrofaunal abundance or diversity patterns. Although the ecological parameters of the benthic macrofauna may be influenced by seagrass biomass and structure, responses differ between epifauna and infauna.