Zooplankton community structure is often characterized by using traits as a function of environmental conditions. However, trait-based knowledge on Southern Ocean mesozooplankton is limited, particularly regarding size and elemental composition. Nine stations around the northern Antarctic Peninsula were sampled during austral autumn to investigate the spatial variability in mesozooplankton taxonomic composition, size structure and stoichiometry in relation to environmental predictors, but also to the abundance of Antarctic krill and salps. The mesozooplankton communities around the South Shetland Islands were dominated by small copepods, mainly Oithonidae and Oncaeidae, while stations along the frontal zones and the Weddell Sea revealed a higher proportion of larger organisms. Spatial differences in taxonomic composition and size structure were significantly altered by salp abundance, with stronger impact on small-sized copepods. Furthermore, taxonomic composition was significantly related to temperature and total carbon but not chlorophyll a, indicating reduced relevance of phytoplankton derived food during autumn. Bulk mesozooplankton stoichiometry, however, showed no significant relation to environmental conditions, mesozooplankton size structure or dominant taxa. Our results indicate that aside from bottom-up related drivers, top-down effects of salps may lead to mesozooplankton communities that are more dominated by larger size classes with potential consequences for trophic interactions and nutrient fluxes.