From the Indian coast only limited data are available on the benthic fauna of the seagrass communities. In this study, seasonal variation in the distribution of macrobenthos and influence of environmental param-eters was explored at four seagrass beds and two mangrove stations along the Minicoy Island, Lakshadweep, India, from September 1999 to August 2001. A total of 160 macrobenthic species from eight major groups represented the macrofauna of the Minicoy Island. Of the identified taxa, molluscs 70 (gastropods 41.46%, bivalves 7.5%), polychaetes 27 (16.88%), crustaceans 30 (18.75%), echinoderms 11 (6.88%) and remaining others. Average seasonal abundance of benthic macrofauna ranged from 219 to 711 ind./m2, species di-versity varied from 1.45 to 3.64 bits per individual, species richness index ranged from 4.01 to 26.17, even-ness 0.69 to 1.66. In general, the higher abundance and species diversity was noticed in southern seagrass stations and northern seagrass stations, but in the mangrove stations comparatively low species diversity was observed. Three-way analysis of variance indicated that all communities resulted as being significantly different between seagrass and mangrove station, mainly when the seasonal interaction was considered. Multivariate analyses were employed to help define benthic characteristic and the relationship between environmental parameters at the six monitoring stations. Results of cluster analyses and multidimensional scale plot suggest that for mangrove region, different physiographic provinces, lower salinity, dissolved oxy-gen and sediment biotic structure have a higher influence on the species composition and diversity than other oceanographic conditions.