Microalgae, the ocean's primary producers, have proven a large capacity for adaptation, but the implications for species interactions are rarely examined. In a 2-year experiment, we exposed the marine diatom Chaetoceros tenuissmus to warming and examined the responses of its mutualistic bacterial community. The diatom adapted to warming by increasing its temperature optimum and maximum growth rate, whereas the microbiota increased its maximum growth rate without changing its temperature optimum. Rhodobacteria dominated the diatom-associated communities at ambient temperatures and this dominance did not diminish under warming conditions. Extinctions occurred in low-abundance genera, but under warming conditions, new partners appeared. The warming consortium was stable when transplanted to ambient temperatures, indicating a strong association. Duration of exposure to temperature appeared relevant, highlighting the consequences of short-warming events. Our results agree with predictions that long-term evolution of asymmetric mutualistic associations increases strength and diversity, particularly under warming.