The Costa Rica Dome (CRD) is a wind-driven upwelling feature in the eastern tropical Pacific that supports unusually high concentrations (. 106 cells mL21) of the picocyanobacteria Prochlorococcus and Synechococcus. To understand what causes this unusual phytoplankton bloom, we conducted a comprehensive survey of the hydrography, picophytoplankton population structure, and trace metal chemistry of the CRD and surrounding oligotrophic and equatorial upwelling waters. Based on size-fractionated chlorophyll, picoplankton dominated phytoplankton biomass in the region, and the three water regimes sampled supported different assemblages of Prochlorococcus, Synechococcus, and eukaryotic picophytoplankton. Cobalt (Co), a required nutrient for cyanobacteria, was strongly complexed in surface waters and was at least twice as high in the photic zone of the CRD than in surrounding waters. In contrast, iron (Fe) and manganese (Mn) levels were comparable in and outside the CRD. Synechococcus clades II and CRD1 and Prochlorococcus ecotype eMIT9312 (high light II) were the dominant genotypes throughout the region, as assessed by quantitative polymerase chain reaction assays. The composition of less abundant Synechococcus clade subpopulations differed in and outside the CRD and within the CRD. Co, mixed layer depth, and temperature were the important drivers of both total Synechococcus abundance and cyanobacterial community composition. This supports a model whereby the combination of upwelled macronutrients, high concentrations of complexed Co, and Fe and Mn scarcity in the warm, shallow mixed layer of the CRD limit larger phytoplankton and induce dense concentrations of picocyanobacteria. Globally, we suggest that trace metals influence phytoplankton distributions at both the broad (cyanobacterial vs. eukaryotic) and the fine (ecotype-level) taxonomic levels.