Mesoscale features within the Gulf of Mexico (GOM) are known to influence zooplankton dynamics. Here we describe the composition of the zooplankton assemblage off shelf during summer in relation to environmental conditions, with emphasis on hyperiid amphipods and salps. Zooplankton samples were collected in summer of 2015 and 2016 in the central and southern GOM and in the Yucatan Channel in 2015. Two anticyclonic gyres were present in the north and less intense coupled cyclonic-anticyclonic gyres in the south. Zooplankton abundances differed temporally and spatially. Copepods were the dominant group (>55% of total abundance), while several less abundant taxa contributed to inter-annual and spatial differences. Amphipods and salps comprised <3% and their abundances were positively correlated. Fifty-six hyperiid and 10 salp species were identified. The dominant amphipod species were: Lestrigonus bengalensis (summer 2015), Anchylomera blossevillei and Primno spp. juveniles (summer 2016). Dominant salp species were Ihlea punctata, Iasis cylindrica and Thalia spp. Lower salp and amphipod species richness and abundance were associated with anticyclonic structures. Spatial and temporal differences were partly associated with symbiotic relationships between the groups. This study supports previous evidence of high spatial and temporal variability in zooplankton abundance in off-shelf waters of the GOM.