Marine communities are subject to alterations in environmental conditions, due to both natural variability and climate change. For instance, a rapid increase in sea surface temperature (SST) can modify spatial distribution patterns and abundances of reef fishes and therefore alter the overall diversity, structure, and functioning of these communities. Trait-based approaches may accurately detect community responses to such environmental changes, because species traits should reflect resource and habitat requirements. Here, we investigated temporal variability in reef fish trait composition and thermal affinity and assessed whether shifts are linked to recent ocean warming. We combined species traits related to feeding, growth, and survival with abundance data on reef fish from underwater visual census at 7 islands of the Southwestern Atlantic subtropical transition zone. All islands exhibited gradual trait reorganization from fish assemblages dominated by large-size species at the beginning of the time period to small, cryptobenthic species towards the end. The temporal changes in community weighted mean traits and the community thermal index were related to SST, indicating a numerical response of species to climatic variations. Tropical species are slowly becoming more abundant over time, while temperate species are becoming less abundant, reflecting an initial change in fish composition in this transition zone. These results have ecological implications leading communities to a faster turnover, lower food-chain complexity, and higher vulnerability to change. We highlight the importance of integrating traits and abundance time series data for a holistic understanding of reef dynamics and community responses to environmental variation, including global warming.