Eukaryotic phytoplankton are responsible for at least 20% of annual global carbonfixation.Their diversity and activity are shaped by interactions with prokaryotes as part of complexmicrobiomes. Although differences in their local species diversity have been estimated, westill have a limited understanding of environmental conditions responsible for compositionaldifferences between local species communities on a large scale from pole to pole. Here, weshow, based on pole-to-pole phytoplankton metatranscriptomes and microbial rDNAsequencing, that environmental differences between polar and non-polar upper oceans moststrongly impact the large-scale spatial pattern of biodiversity and gene activity in algalmicrobiomes. The geographic differentiation of co-occurring microbes in algal microbiomescan be well explained by the latitudinal temperature gradient and associated break points intheir beta diversity, with an average breakpoint at 14 °C ± 4.3, separating cold and warmupper oceans. As global warming impacts upper ocean temperatures, we project that breakpoints of beta diversity move markedly pole-wards. Hence, abrupt regime shifts in algalmicrobiomes could be caused by anthropogenic climate change.