The Panamanian Pacific is under the influence of natural environmental changes, such as the coastal upwelling and manifestation of El Niño. These events can have severe implications for the biological resources. In this study we characterized the hydrological changes in the Gulf of Panama as related to their seasonality and annual variability. The intensity of the upwelling was assessed using sea surface temperature data. We also evaluated the coral genetic diversity for the coral Pocillopora damicornis. There were obvious changes in the hydrological and biological parameters monitored in the Gulf of Panama as result of the upwelling. The historical analysis of upwelling in the Gulf of Panama indicated that the upwelling occurs in pulses related to sea surface temperatures. In conclusion, sea surface temperature is the best quantitative estimate of upwelling intensity in the Gulf of Panama. The electrophoretic analysis of isozymes in the coral Pocillopora damicornis in Panama suggest the existence of a wider genetic diversity in the thermically stable water of the Gulf of Chiriquí and in areas of moderate upwelling such as Iguana Island in the Gulf of Panama. This contrast with the limited genotypic diversity found in areas of strong upwelling such as the Pearl Islands and the Panama Bay.
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