Oceanic islands and seamounts are considered biodiversity hotspots. Here, we present a taxonomy and community analyses of hyperiid amphipods collected near oceanic islands and over seamounts of the Juan Fernández Archipelago and Desventuradas Archipelago in the South-east Pacific. Both archipelagos are separated by about 800 km over the meridional gradient, suggesting the existence of different hyperiid communities because of apparent geographic isolation and distinctive oceanographic characteristics between regions. To test this hypothesis, zooplankton samples were collected from 19 stations during the CIMAR 22 ‘Oceanic Island’ cruise in October–November 2016. In total, 56 species of hyperiids were found, of which Phrosina semilunata, Lestrigonus schizogeneios, Hyperietta stephenseni, Hyperioides longipes, Phronimella elongata and Primno latreillei were the most abundant and recurrent species. The species richness (S), Shannon–Wiener diversity (H’) and dominance (D) of both the archipelagos were not significantly different. Additionally, except for a small group of rare species, the species composition was similar in both areas. Most species showed greater abundances than those observed in the coastal upwelling zone off Chile, whereas shared species between regions suggested the presence of a single biogeographic unit comprising the coastal transition zone and oceanic area off Chile within which both archipelagos are included. Correlation analysis indicated that salinity was the best predictor for the community structure, which provides evidence that the contributions of previously described water masses of the South-east Pacific may influence the spatial distribution and composition of the hyperiid community.