Significance The oceans are populated by an astronomical number of predominantly uncultured microbes, which altogether guarantee ecosystem function. Unicellular eukaryotic predators represent basal links in marine food webs and have so far been predominantly characterized as a functional group, despite having different ecologies and evolutionary histories. In order to better understand the ecoevolution of the ocean’s smallest predators, we have investigated four species belonging to an uncultured cosmopolitan family: marine stramenopiles (MAST)-4. Using state-of-the-art single-cell genomics and metaomics approaches, we found that members of this predatory family have different distributions in the surface ocean and different genes to degrade food, which likely represent niche adaptations. Our work highlights the importance of understanding the species-level ecology and genomics of tiny ocean predators.