To successfully persist in changing climates, organisms must track favorable conditions, often through narrow geographic corridors of suitable habitat. However, corridors facilitating population connectivity may be sensitive to climate disruption. Deterioration of once-valuable corridors can have consequences for gene flow, metapopulation persistence, and climate-driven range shifts. To quantify the sensitivity of ecological corridors to climate change, I integrated large-scale geospatial modeling with finite stochastic process theory to develop and validate statistical models of population connectivity for Japan’s flora. After modeling the geographic niche space of all of Japan’s plant species and reprojecting them under future climates, I evaluated the spatiotemporal dynamics of population connectivity using spatial absorbing Markov chains. Aggregating these predictions allowed me to identify and map ecological corridors that are at risk of climate degradation and those that facilitate climate-driven redistribution of threatened, invasive, and culturally meaningful plant species.