Dinitrogen (N2) fixation by the keystone marine cyanobacteria genera Trichodesmium and Crocosphaera is a major source of bioavailable new nitrogen supporting open ocean food webs and biogeochemical cycles. Although multiple studies have suggested that cyanobacteria N2 fixation rates will increase dramatically with future rising carbon dioxide (CO2), all of these relied on the same limited set of culture isolates. We grew seven cyanobacteria strains from the Atlantic and Pacific Oceans over a wide range of CO2 concentrations, and measured their N2 fixation and growth rates. Here we show large taxon-specific differences in their N2 fixation CO2 functional response curves, demonstrating that particular strains within each genus are adapted to grow and fix N2 at specific CO2 concentrations. Application of kinetic constants from these curves to biogeochemical models of surface seawater CO2 suggests that high CO2-adapted strains may be favored in the future acidified ocean. Our results imply that CO2 could be a previously unrecognized selective force shaping the community composition and diversity of N2-fixing cyanobacteria over both ecological and geological timescales.