Baseline ecological studies of Pondicherry mangroves are important for monitoring, management and conservation of mangrove ecosystems. A brachyuran crab faunal assemblage at four stations of Pondicherry mangroves is described and monthly samplings were made during September 2008 – August 2009. Totally 22 species of brachyuran crabs belonging to 12 genera and 5 families were recorded crabs belonging to the family Portunidae and Ocipodidae are most dominant group represented by total of 16 species. Six species considered are as a commercially important and out of which, on three species Scylla serrata, Thalamitta crenata and Portunus sanguinolentus are catch large quantities from stations 1 and 2. Portunus pelagicus, P. sanguinolentus and T. crenata were totally absent in stations 3 and 4. Population densities of brachyuran fauna ranged from 29 -71 ind. m2, the diversity ranged from 0.96 -2.18 bit. ind -1, the richness varied from 0.42 -0.74, and the evenness varied from 0.41 -.072. Maximum diversity values were recorded during post monsoon. The crab community recorded was analyzed by univariate and multivariate statistical techniques. Crab community structure was correlated with vegetation structure, and environmental factors were positively correlated with surface water pH, salinity, tree dominance, tree diversity and tidal inundation and negatively correlated with sulphide, organic matter, senescent leaves and decaying leaves, suggesting that the mangrove vegetation is important to the crab fauna as a habitat and food supply.