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Abstract In this study, we combined “reciprocal transplant experiments,” cell‐sorting, and metagenomics to understand how phytoplankton adapt to differences in phosphate availability and the implications for nutrient uptake rates. Reciprocal transplant experiments were conducted on six stations ranging from cold, nutrient‐rich water in the Labrador Sea to warm, extremely P‐deplete water in the Sargasso Sea. In most cases, the direct impact of environmental conditions and likely P availability was the strongest control on phosphate uptake. However, especially the transplant experiments between the northern and southern stations revealed that there are situations where changes in community composition and functional genes have an important effect on uptake rates. Phytoplankton lineages responded uniquely to changing environmental conditions. The picoeukaryotic phytoplankton P uptake response was strongly regulated by the phosphate concentration, whereas the effect of community composition was larger forProchlorococcusandSynechococcus. In support, we found a tight negative relationship between ambient phosphate concentration and the frequency of P acquisition genes in bothProchlorococcusandSynechococcus, and such differences in genome content could be linked to lineage‐specific shifts in uptake rates. Linking genes with ocean biogeochemistry is a major scientific and technical challenge and most studies rely on correlations between genotypes and environmental conditions. However, our study demonstrates how reciprocal transplant experiments are a possible tool for understanding the relative role of environmental condition vs. plankton diversity in regulating important open ocean ecosystem processes.