The importance of marine phytoplankton in food webs and biogeochemical cycles makes the study of prokaryotic and eukaryotic phytoplankton species essential to understand changes in the global ecosystem. As plankton is transported by ocean currents, its community composition varies. Some species are abundant in contrasting environments, which raises the question of the genomic basis of their adaptation. Here we exploit the cosmopolitan distribution of the eukaryotic picoalgae Bathycoccus prasinos to investigate its genomic variations among temperate and polar populations. Using multiple metagenomic data, we found that ~5% of genomic positions of B. prasinos are variable, with an overwhelming majority of biallelic patterns. Cold and temperate waters are clearly associated with changes in variant occurrences including striking differences at some nonsynonymous positions of several genes. Data from transitional waters showed more balanced polymorphism at most of these positions. The comparison of mesophilic and psychrophilic gene variants of this species suggests that its adaptation to cold waters may involve few amino acid changes at positions of protein structures critical for physical and functional properties. These results provide new insights into the genomic diversity and temperature-associated amino acid changes of a cosmopolitan eukaryotic planktonic species.