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Ongoing climate change is predicted to trigger major shifts in the geographic distribution of marine plankton species. However, it remains unclear whether species will successfully track optimal habitats to new regions, or face extinction. Here we show that one significant zooplankton group, the radiolaria, underwent a severe decline in high latitude species richness presaged by ecologic reorganization during the late Neogene, a time of amplified polar cooling. We find that the majority (71%) of affected species did not relocate to the warmer low latitudes, but went extinct. This indicates that some plankton species cannot track optimal temperatures on a global scale as assumed by ecologic models; instead, assemblages undergo restructuring and extinction once local environmental thresholds are exceeded. This pattern forewarns profound diversity loss of high latitude radiolaria in the near future, which may have cascading effects on the ocean food web and carbon cycle.