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Interacting species can respond differently to climate change, causing unexpected consequences. Many understorey wildflowers in deciduous forests leaf out and flower in the spring when light availability is the highest before overstorey canopy closure. Therefore, different phenological responses by understorey and overstorey species to increased spring temperature could have significant ecological implications. Pairing contemporary data with historical observations initiated by Henry David Thoreau (1850s), we found that overstorey tree leaf out is more responsive to increased spring temperature than understorey wildflower phenology, resulting in shorter periods of high light in the understorey before wildflowers are shaded by tree canopies. Because of this overstorey-understorey mismatch, we estimate that wildflower spring carbon budgets in the northeastern United States were 12-26% larger during Thoreau's era and project a 10-48% reduction during this century. This underappreciated phenomenon may have already reduced wildflower fitness and could lead to future population declines in these ecologically important species.