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Impacts of long-term climate shifts on the dynamics of intact communities within species ranges are not well understood. Here, we show that warming and drying of the Southwestern United States over the last 25 years has corresponded to a shift in the species composition of Sonoran Desert winter annuals, paradoxically favoring species that germinate and grow best in cold temperatures. Winter rains have been arriving later in the season, during December rather than October, leading to the unexpected result that plants are germinating under colder temperatures, shifting community composition to favor slow growing, water-use efficient, cold-adapted species. Our results demonstrate how detailed ecophysiological knowledge of individual species, combined with long-term demographic data, can reveal complex and sometimes unexpected shifts in community composition in response to climate change. Further, these results highlight the potentially overwhelming impact of changes in phenology on the response of biota to a changing climate.