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Abstract Light penetration through the ocean creates underwater light color niches and photosynthetic organisms use specific strategies to capture light in these niches. The selection pressure for some cyanobacteria strains in the genusSynechococcusthat change color to absorb either blue or green light (chromatic acclimaters, or generalists) is not well understood. Here, we tested the hypothesis that changes in ocean spectra brought about by mixing preferentially selects for generalists within aSynechococcuspopulation. We investigated ocean conditions that led to high proportions ofSynechococcusgeneralists versus specialists in a model ocean column, and compared simulations with in situ metagenomic and physical oceanographic data from major Bio‐GO‐SHIP cruises, supplemented with GEOTRACES and TARA Oceans, as well as the GOOS Argo Program and sea surface height from AVISO. We found that greater mixed layer depths selected for generalists in simulatedSynechococcuspopulations, but did not account for much of the variance in the partitioning of light‐harvesting strategies in situ. Rather, oceanographic signatures for upwelling areas and ocean fronts explained more of the variation betweenSynechococcusgeneralists and specialists in the ocean. Our results motivate further study of the in situ light environments of upwelling zones and ocean fronts, which are currently understudied as potential light‐driven niche habitats.