Seasonal upwelling in the Bay of Panama and along the Pacific coast of Panama in general occurs during the dry season, from January to April. This event leads a reduced water temperatures and high marine productivity. This is the first study of holoplanktonic gastropods from the Pteropoda and Pterotracheoidea in Panama. Holoplanktonic gastropods are mollusks that have managed to develop their complete life cycle in the pelagic zone. These gastropods are known for being potentially good indicators of ocean acidification, as they are highly sensitive to environmental conditions, yet their abundance and distribution in coastal waters are poorly known. Here we documented their diversity and abundance from weekly vertical plankton tows taken during upwelling and non-upwelling seasons at three different sites in the Bay of Panama. Environmental data was collected during the weekly sampling. Gastropods were separated from the samples, counted and identified using morphological criteria based on the general shell morphology, the count of spires and type of eye present. A total of 15,153 organisms were collected from the three sites and belonged to the genera Atlanta, Firoloida and Pterotrachea from the Pterotracheoidea and the genera Cavolinia, Creseis, Paraclione, Clio, Corolla, Diacavolinia, Diacria, Hyalocylis and Limacina from the Pteropoda. The Pterotracheoid genera were equally abundant all year, but the pteropods were generally significantly more abundant during non-upwelling. Overall pteropod abundances were positively correlated with water temperature, dissolved oxygen concentration and pH and negatively correlated with salinity, which reflects the seasonal changes in seawater characteristics.