Jobos and Guayanilla Bays are semi-enclosed bays on the south coast of Puerto Rico. J obos Bay receives some small amounts of raw sewage from two small villages and some wastes from a sugar central. Guayanilla Bay receives some sewage from a town on one shore, hydrocarbon, heavy metals, and carbohydrate addition from a petrochemical complex, and heat from an electrical power generating plant. Species diversity as indicated by the Shannon- Weaver index is higher in Jobos but the lowest values found in either bay are higher than these reported for normal temperate aquatic systems. Numbers of fish species are high (198 for Jobos and 93 for Guayanilla). The greatest similarity between the two bays is between Jobos Inner Bay which is turbid and receives some raw sewage and Guayanilla Thermal Cove which receives heated effluents up to 40°C (s=.526).