Abstract: Morphometric analysis of shell shape and size seems a priori to be a realistic alternative for inter-group discrimination. Analysis of external shell trait measurements of Venerid clam Paphia malabarica of Ashtamudi estuary, a deep estuary unveiled morphological plasticity in the population. The clam population in the barmouth of estuary was found to be morphologically varied from the clam population of upper reaches. The morphotypes displayed variation from 11% to 38% in external shell traits. The phenotypic plasticity can be explained by ecophenotypic variation along a depth gradient with uneven shell thickness and shorter form in deeper part of the estuary near barmouth where wave action and tidal currents were higher and with longer and deeper shells in shallow upper reaches of estuary. Ecological changes in the habitat affect the distribution and abundance of clams in the estuary. Habitat heterogeneity for long period increase genetic variations.