Anthropogenic inputs influence the community structure and activities of microorganisms, which may impinge the functioning of estuarine and coastal ecosystem. The aim of the present study was to understand the influence of dissolved heavy metals (Cr, Mn, Fe, Ni, Cu and Zn) on community structure of cyanobacteria in a nutrient rich tropical estuary, Cochin Estuary (CE), across the southwest coast of India. Dissolved heavy metals were higher in CE during dry season, with Zn as major pollutant.