The surrounding area of the St. Peter and St. Paul Archipelago (SPSPA) (0°55′10″N 29°20′33″W) was investigated in order to verify the physical and chemical influences in species composition and abundance, and the patterns of distribution of phytoplankton in the water column, especially in the thermocline depths. The expedition was held on board the Cruzeiro do Sul Hydro-oceanographic ship, from 21 to 23 July 2010 in two perpendicular and opposite transects. A cylinder-conical net and Niskin bottles were used. Two water masses were identified (Tropical Water and South Atlantic Central Water), and the thermocline depths varied from 40 to 110 m. A total of 128 species of phytoplanktonic organisms were identified, belonging to four phyla. The most conspicuous species was the cyanobacteria Trichodesmium thiebautii; nevertheless, 22 species were considered new registers for the region. The total phytoplanktonic density (1 × 103 to 183 × 103 cells l−1) was low and typical of oligotrophic regions, decreasing slightly with depth. Among the 35 species identified in the vertical distribution, 22 were present in the thermocline depth. The total density of Trichodesmium thiebautii, Oxytoxum longiceps and Protoperidinium minimum had significant correlations with the physical and chemical parameters. These data indicate that SPSPA can be associated to an island mass effect in the local oceanic circulation that mainly affects the physical and chemical characteristics of the surrounding waters. Consequently, these interactions influence the phytoplanktonic community, mainly those located at the end of the photic zone and those that are under the influence of thermocline oscillation.