To compare the diversity and community structure of macrobenthic fauna inhabiting shrimp aquaculture ponds, quantitative samplings using a multilayer cylinder were carried out in culture experimental ponds at Samut Songkhram, along the innermost part of the Gulf of Thailand. A total of 25 species/taxa of macrobenthic organisms were identified from the six aquaculture ponds; four ponds used for active shrimp (Penaeus monodon Fabricius) culture and two ponds planted with mangrove stands (Rhizophora mucronata Lamarck). The dominant species belonged to three taxonomic categories; that is, (1) sedentary, tube-dwelling spionid, Polydora sp., free-living nereid, Perinereis sp., and some other polychaetes (Annelida), (2) gastropods such as Cerithidea cingulata, Cerithium coralium, Thiara riqueti, and Stenothyra spp. which live on the surface or in the shallow layer of the substratum (Mollusca), and (3) barnacles, Balanus sp., and some small arthropods such as ostracods, copepods, harpacticoids, amphipods, and dipterans (Arthropoda). Maximum density and biomass exceeded 10,000 individuals/m² and 600 g/m², respectively, and gastropods were the most dominant and representative taxa in most of the ponds. Species composition was clearly distinguished between the shrimp culture ponds and the mangrove planted ponds. Population density, species richness and species diversity indices of macrobenthic organisms in the bottom of the mangrove planted ponds were significantly higher than those of the shrimp culture ponds, suggesting that mangrove was important for maintaining and increasing the biodiversity. There was a tendency that epibenthic mollusks and arthropods decreased evidently as the depth increased from the surface to the deeper layers, while annelids were found not only in the surface layer but also in the moderately deeper layer. A possibility that Penaeus monodon fed on some macrobenthic organisms under the cultured conditions was discussed.