Calanoid copepods (CC) are key contributors to the biological carbon pump and pelagic trophic dynamics. The deep-water regions of Perdido and the Bay of Campeche in the western and southern Gulf of Mexico (GM), respectively, differ in hydrography and productivity, leading to potential differences in copepod biomass and community structure. Zooplankton (0-200 m) were collected from the shelf edge to the deep-water region during the winter and summer autumn 2016. Calanoids contributed 38-60% of total zooplankton biomass and 55-70% of overall copepod abundance. The Bay of Campeche had the highest total zooplankton biovolume (287±120 ml 1000 m−3) and total mean copepod abundance (CC and non-calanoids ~146,000 ind. 1000 m−3) during summer-autumn, likely resulting from cross-shelf nutrient transport fueling local productivity. Adult females dominated calanoid numerical abundance (43-50%), thus suggesting a high reproductive potential. Cluster analysis showed differences between seasons (~40% dissimilarity) but not regions. Environmental conditions explained 22% of the variability in community composition; the winter assemblage was significantly related to oxygen concentrations, whereas the summer-autumn community was related to warmer conditions and higher integrated chlorophyll-a concentrations. The CC community responded to seasonal changes more than regionally related hydrographic differences, with likely implications for organic matter cycling and export.