The aim of this study is to assess small-scale variations in and spatial comparisons among the composition, distribution and abundance of the main zooplankton groups in the Saint Peter and Saint Paul Archipelago (SPSPA). Plankton samples were collected in May 2008 by net with a 300 µm mesh size. Sampling was carried out at two stations, Inner and Outer, during five consecutive days in the early morning and late afternoon. A total of 153 zooplankton taxa were identified. Copepoda was the most abundant and frequent group (with 49 species identified). Exocoetidae (Teleostei) eggs were also present in large numbers. No significant differences were found between stations or between day and night samples. The observed biomass was low; however, it was superior to that observed in the open ocean. The density of zooplankton was also low, but it increased slightly during the night. Indicator species for upwelling, such as Phaenna spinifera and Flaccisagitta hexaptera, were observed. We conclude that physical factors are important for structuring the SPSPA zooplankton community.