As part of the French Joint Global Ocean Flux Study Etude du Broutage en Zone Equatoriale program, we investigated the distributions of microorganisms (bacteria and protists <200 μm) in the upper 120 m of the equatorial Pacific from 8°S to 8°N, along 180°. Population distributions, determined by a combination of flow cytometry, microscopy and spectrofluorometry, were closely related to physical features across the study site. Phytoplankton biomass, ranging from 1.2 to 34.2 μg C L⁻¹ and averaging 15.5 μg C L⁻¹, was most enhanced in the divergence zone. Carbon to chlorophyll ratios were also enhanced in the divergence zone and showed distinct latitudinal variations. Heterotrophic biomass, excluding ciliates, was patchy across the area, ranging from 5 to 36 μg C L⁻¹ and averaging 13 μg C L⁻¹. Prokaryotic species (Prochlorococcus spp., Synechococcus spp., and heterotrophic bacteria) showed similar patterns of abundance, with the main feature being their distributional asymmetry to the south of the equator. Both autotrophic and heterotrophic biomass were enriched in the convergent zone at 4°–5°N between the South Equatorial Current and the North Equatorial Counter Current. Heterotrophic biomass exceeded phytoplankton biomass in the more nutrient-impoverished waters to the north and in the branch of a tropical instability wave eddy. Microplankton represented only a small portion of the total autotrophic carbon and was comprised mostly of dinoflagellates. Large species dominated the relatively modest diatom biomass. Food web interactions and biogeochemical fluxes in the central equatorial Pacific may be significantly influenced by temporal and spatial variability of the microbial community associated with physical features of the region.