The north-western Mediterranean Sea's high biodiversity originates from a mixture of temperate and subtropical species. Large-scale warming has been detected through northward range shifts of ‘warm-water’ species, and mass-mortality events for ‘cold-water’ invertebrates. Marine caves are affected in a more subtle way. By monitoring endemic species of cave mysids (Crustacea) and comparing our results with data in the literature, we observed a strong decline in one species, coupled with the success of another. Near Marseille (France), this phenomenon began while two major thermal anomalies were reported. Different tolerances to temperature were demonstrated by both the species distribution ranges and laboratory experimentation. We provide a possible physiological explanation for populations of cold stenothermal species of endemic cave mysids being replaced by congeners of warmer affinities, with a high risk of extinction. We also found strong support for the view that Mediterranean marine biodiversity is already under the threat of global warming.