Bacteria-microalgae interaction shapes carbon cycles in the pelagic ocean. The biochemical mechanisms underlying their interactions become increasingly known, but whether these ubiquitous interdomain interactions may drive bacterial evolution has not been illustrated. To test this hypothesis, we sought to determine the population structure of roseobacters colonizing the phycospheres of coexisting microalgal cells. A few environmental factors including nutrient availability, interactions with phages and phytoplankton are known to drive roseobacter population differentiation. To single out diatoms from other confounding factors that may drive roseobacter evolution, populations associated with diatoms sampled from a single seawater sample were analyzed. Nanopore sequences in PRJNA764816 Illumina sequences in PRJNA691705