Accounting for 40 percent of the earth's surface, oligotrophic regions play an important role in global biogeochemical cycles, with microbial communities in these areas representing an important term in global carbon budgets. While the general structure of microbial communities has been well documented in the global ocean, some remote regions such as the Western Tropical South Pacific (WTSP), remain fundamentally unexplored. Moreover, the biotic and abiotic factors constraining microbial abundances and distribution remain not-well resolved. In this study, we quantified the spatial (vertical and horizontal) distribution of major microbial plankton groups along a transect through the WTSP during the austral summer of 2015, capturing important autotrophic and heterotrophic assemblages including cytometrically determined abundances of non-pigmented protists (also called flagellates). Using environmental parameters (e.g. nutrients and light availability) as well as statistical analyses, we estimated the role of bottom-up and top-down controls in constraining the structure of the WTSP microbial communities in biogeochemically distinct regions. At the most general level, we found a typical tropical structure, characterized by high abundances of Prochlorococcus at the surface, a clear deep chlorophyll maximum at all sampling sites, and a deep nitracline. Despite their relatively low abundances, picophytoeukaryotes (PPE) accounted for up to half of depth-integrated phytoplankton biomass in the lower euphotic zone. While present at all stations, Synechococcus accounted for only 2 % and 4 % of total phytoplankton abundance and biomass, respectively. Our results show that the microbial community structure of the WTSP is typical of highly stratified regions, and underline the significant contribution to total biomass by PPE populations. Strong relationships between N2 fixation rates and plankton abundances demonstrate the central role of N2 fixation in regulating ecosystem processes in the WTSP, while comparative analyses of abundance data suggest microbial community structure to be increasingly regulated by bottom-up processes under nutrient limitation, possibly in response to shifts in abundances of high nucleic acid bacteria (HNA).