An attempt has been made to elucidate the effects of pollution on the distribution, abundance and diversity of chaetognaths inhabiting the harbour and neritic waters of Visakhapatnam (East Coast of India). Nine species were recorded, out of which three species were common both in harbour and neritic waters. Sagitta bedoti was found to be the most dominant and was present throughout the year. High percentage of S. hipsida and S. robosta and to some extent  S.bombayensis  are the organisms sustain the adverse conditions of water quality S. oceanica and Krohnitta pacifica  are present only in the clean environment.