AbstractThe effects of global change are particularly serious in areas where range shifts of species are physically constrained such as the Ligurian Sea, which is one of the coldest sectors of the Mediterranean. In this basin, historical information on water temperature (from the sea surface down to 75 m depth) dates back to the 1950s. Early studies also recorded warm‐water species occurrence. Thanks to these data we provide the first detailed characterization of water temperature variation from 1958 up to 2010 in the layer 0–75 m depth. We coupled this analysis with the available information on rocky reef epibenthic communities (literature review from 1955 to 1964 and field data from 1980 to 2010). The analysis of water temperature revealed several patterns of variation: a cooling phase from 1958 to 1980, a phase of rapid warming from 1980 to 1990 and a phase of slower warming from 1990 to 2010. Inter‐annual variation in temperature increased over the entire period for the water layer down to 20 m. Warm‐water native and alien species richness increased during the warming phases. Literature estimates suggest a decrease in warm‐water native species richness during the cooling phase. The analysis of quantitative data collected in the early 1990s and late 2000s indicated a decrease in the cover of warm‐water native species on shallow rocky reefs and an increase in deeper waters. We argue that increased inter‐annual variation in water temperature may disadvantage native warm‐water species in shallow waters. Our results indicate that the effect of temperature rises in cold, constrained basins may be more complex than the simple prediction of species changing their geographical range according to their thermal limits.