Tropical coastal areas are amongst the most diverse ecosystems in the world. However, there are quite a few coasts that have rarely been studied for their macro-benthic diversity. The Indian coastline presents one such gap area. Two sub-parallel coastlines of India have a wide latitudinal span (8–23°N) and strikingly different physiographic environments. While the east coast receives a high siliciclastic input from large river systems flowing to the Bay of Bengal with fluctuating salinity, the west coast has a large shelf area and high productivity of the Arabian Sea. Such difference enables us to evaluate the effect of regional environmental parameters on marine molluscan diversity and distribution in an intra-tropical setting. Because of the wide latitudinal range, it is also possible to assess if spatial difference in species richness in such a regional scale follows the large-scale biodiversity pattern such as Latitudinal Biodiversity Gradient (LBG) despite inherent environmental variation. We used species distribution of marine bivalves, compiled using bioSearch and the Ocean Productivity database, to address this question. Our results show that intra-tropical species richness of marine bivalves is guided primarily by regional environmental parameters. Even with identical latitudinal extent, higher nutrient availability and larger shelf area, the west coast has significantly lower richness than the east coast; among environmental variables, productivity, salinity and coastline length emerged as significant predictors of species diversity. Moreover, a positive influence of a South Asian biodiversity hotspot on east coast fauna and a negative impact of the oxygen-depleted condition of Arabian Sea on west coast fauna, may have a significant contribution in developing such coastal variation in species richness. The latitudinal variation in species richness did not follow LBG. In contrast to the coast-specific diversity difference, species composition is not found to be dictated by coastal affiliation. The composition corresponds primarily to physiographic conditions. We identified three distinct eco-regions (north-western, southern, north-eastern) with characteristic species composition corresponding to unique physiography and productivity mechanism. The NW region has low siliciclastic input and high productivity associated with upwelling during winter cooling. The NE region has a distinctly high riverine input and salinity fluctuation. The southern region, in contrast, has well developed reefal system with moderate variation in salinity. Such correspondence underscores the importance of the regional environment in dictating the species diversity and distribution in the shallow marine realm.