Oceans connect all life and affect climate worldwide, and interestingly, the ocean’s smallest residents have a huge role in this process. The ocean microbiota modulates global biogeochemical cycles, which influences energy balance in the atmosphere. Unfortunately, the underlying factors structuring the ocean microbiota are unclear, and better understanding is needed to help combat the effects of global climate change. A recent study examined the ecological mechanisms shaping the smallest surface-ocean microbiota: prokaryotes and picoeukaryotes. Researchers identified patterns in DNA sequencing data collected by two global ocean expeditions, Malaspina-2010 and Tara Oceans. Their results showed that different ecological mechanisms affect prokaryotes vs. picoeukaryotes. While picoeukaryotes were largely structured by dispersal limitation, displaying higher differentiation between communities, prokaryotes were structured by a combination of temperature-driven selection, dispersal limitation and random drift. The results suggest that it is important to consider the unique mechanisms affecting each component of the ocean microbiota, providing insight into the current and future composition of the ocean’s tiniest microbes as they react to climate change.