Marine zooplankton play key roles in the transfer of energy to higher trophic levels and the removal of CO2 from the atmosphere through the sedimentation of inorganic and organic carbon compounds included in their fecal pellets. Therefore, differences in the zooplankton groups driven by climate variations could influence the biogeochemical cycles at large oceanic scales. As a contribution to this topic, we analyzed the zooplankton groups in the Bay of La Paz, Gulf of California, Mexico, a highly dynamic basin characterized by its high biological productivity. We used information gathered during multidisciplinary research cruises in the summers of 2008 and 2009. The results showed differences in the hydrographic parameters between both summers, with a higher temperature recorded in 2009. The zooplankton groups showed that the calanoid copepods were the most abundant; however, there were important differences in the relative abundance of the rest of the analyzed groups as an effect of the temperature distribution along the study area, which was confirmed by multivariate statistical methods. These temperature changes were associated with increased gelatinous zooplankton (Cnidaria, Chaetognatha, Appendicularia, and Ctenophora) in 2009 in a region where the temperature was higher, possibly as a result of changes in food (phytoplankton) availability.