The subtropical region of the Southeast Pacific exhibits a strong onshore-offshore gradient in hydrographic conditions and biological production from the eutrophic upwelling zone to the ultra-oligotrophic oceanic area in the central South Pacific gyre (SPG). Across this gradient, zooplankton must cope with either gradual or abrupt changes in environmental conditions. Here, the distribution and diversity of hyperiid amphipods were assessed over this gradient in the upper 1000 m in relation to temperature, salinity, oxygen, chlorophyll-a, sea level anomalies, the bulk of mesozooplankton biomass and the biomass of salps, siphonophores, and other hydrozoans during October/November 2015 from the coastal zone off Chile (27°00‵ S, 70°52‵ W) to near Easter Island within the SPG (27°10‵ S, 109°20‵ W). The most frequent and abundant species were Hyperioides longipes Chevreux, 1900, Eupronoe minuta Claus, 1879, and Hyperioides sibaginis (Stebbing, 1888). Significant changes in abundance and community structure across the gradient with respect to the evaluated environmental variables and significant correlations of 17 hyperiid species with the gelatinous category other hydrozoans were found. These changes were closely linked to previously defined zonation patterns, which contained distinct species assemblages and a unique dominant species per zone. These zones represented ecoregions based on diversity patterns of hyperiids and other shared species among such ecoregions suggesting a possible ecological connectivity among the zones, promoted by mesoscale eddies travelling westward from the coastal upwelling zone to offshore waters. Environmentally forced zonation and the interactions with mesoscale features are thus suggested as the driving processes maintaining spatial patterns of diversity of the hyperiid community in the Southeast Pacific.