The network of roots and rhizomes of seagrasses plays an important role in coastal ecosystems by anchoring the substrate firmly, controlling the biogeochemistry of the sediments and providing habitat for many infaunal organisms. The purpose of this study was to compare five seagrass communities in southern Thailand in terms of species composition, belowground biomass, redox potential and the abundance of the dominant bivalve Pillucina vietnamica. The communities of Halophila ovalis, Cymodocea rotundata, Thalassia hemprichii, H. ovalis with C. rotundata and C. rotundata with T. hemprichii were studied. Belowground biomass, redox potential, bivalve abundance and bivalve size differed among communities and depths (P < 0.05). The redox potential in vegetated areas was lower than in bare sand, showing that seagrass roots trapped more organic matter than did bare sand. The lowest redox potential was in a monospecific patch of the branching root species, C. rotundata. The abundance of P. vietnamica in vegetated areas was lower than in bare sand (P < 0.05). Pillucina vietnamica was relatively large in size in the monospecific stands of C. rotundata and T. hemprichii, where relatively high root biomass and belowground biomass, respectively, were found. Our results suggest that seagrass promotes anoxic conditions belowground by trapping sediment but could obstruct the burrowing activity of lucinids, as dense populations of lucinids occurred mainly in bare sand. However, seagrass also provided shelter for lucinids, as larger bivalves were found in seagrass areas. The interactions among belowground seagrass parts, the biogeochemistry of sediments and the lucinids are highly complex and merit further study.