Significance The free-living cyanobacterium Trichodesmium is an important nitrogen-fixer in the global oceans, yet virtually nothing is known about its molecular evolution to increased CO ₂ . Here we show that Trichodesmium can fix a plastic, short-term response upon long-term adaptation, potentially through genetic assimilation. We provide transcriptional evidence for molecular mechanisms that parallel the fixation of the plastic phenotype, thereby demonstrating an important evolutionary capability in Trichodesmium CO ₂ adaptation. Transcriptional shifts involve transposition and other regulatory mechanisms (sigma factors) that control a variety of metabolic pathways, suggesting alterations in upstream regulation to be important under genetic assimilation. Together, these data highlight potential biochemical evidence of genetic assimilation in a keystone marine N ₂ -fixer, with broad implications for microbial evolution and biogeochemistry.