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Abstract Flowering phenology can vary considerably even at fine spatial scales, potentially leading to temporal reproductive isolation among habitat patches. Climate change could alter flowering synchrony, and hence temporal isolation, if plants in different microhabitats vary in their phenological response to climate change. Despite the importance of temporal isolation in determining patterns of gene flow, and hence population genetic structure and local adaptation, little is known about how changes in climate affect temporal isolation within populations.Here, we use flowering phenology and floral abundance data of 50 subalpine plant species over 44 years to test whether temporal isolation between habitat patches is affected by spring temperature. For each species and year, we analysed temporal separation in peak flowering and flowering overlap between habitat patches separated by 5–950 m.Across our study species, warmer springs were associated with more temporal differentiation in flowering peaks among habitat patches, and less flowering overlap, increasing potential for temporal isolation within populations.Synthesis. By reducing opportunities for mating among plants in nearby habitat patches, our results suggest that warmer springs may reduce opportunities for gene flow within populations, and, consequently, the capacity of plant populations to adapt to environmental changes.