Few studies have quantitatively compared benthic macrofaunal assemblages between different tropical intertidal habitats over differing spatial scales. The present study uses spatially nested material from vegetated (seagrass) and non-vegetated (mudflat) habitats in SW Thailand to address this issue. Polychaetes were the numerically dominant component of benthic assemblages throughout the region, comprising over 74% of the total macrofauna. Despite great within-site and sample variation, based on species diversity, polychaete assemblages were mostly site-specific. Not so visibly obvious were the evident differences in polychaete assemblages between habitats. The spatial pattern of polychaete diversity is explored.