Phenotypic plasticity in Paphia malabarica was analysed using shell morphometry and molecular analysis. Intra-specific variability reflects changing ecophysiological requirements and constraints with body size, alongside genetic and environmental influences on shell morphology. External shell trait measurements in the morphotypes displayed phenotypic plasticity. Molecular analysis using Internal Transcribed Spacers sequence region of nuclear ribosomal DNA revealed that the genetic distance between the Paphia populations of the estuary was not significant to consider them as genetic variants. Phylogenetic analyses confirmed that the morphotypes are sister clades with cent percent bootstrap value. Hence, it can be authenticated that the morphotypes are clams exhibiting phenotypic plasticity and they are ecophenotypes resulted from the environmental factors. The morphometrics can quantify a trait of evolutionary significance, and deduce something of their ontogeny or evolutionary relationships by detecting changes in the shape of the organism.