Paramuricea clavata is an ecosystem engineer, structuring hard bottom communities in the Mediterranean Sea, from 10 to 200 m depth. For more than 2 decades, shallow populations of P. clavata have been impacted by marine heatwaves, resulting in massive mortality events. Recently, a new dense population characterized by the tallest colonies ever recorded (up to 1.80 m) in the Mediterranean Sea was discovered between 50 and 60 m depth. Here, we analyzed the size and genetic structure of this ‘deep giant population’ and conducted a reciprocal transplant experiment with a shallow population inhabiting the same area to test for local adaptation. The experiment showed no significant difference in the survival rate despite the high temperatures registered in the shallow area. Nevertheless, we observed a significant differentiation by depth in this area, with low estimates of gene flow. The particular local oceanographic conditions could lead to a relative isolation of the population. In conclusion, the reduced connectivity of this newly discovered giant population with shallower ones questions its potential role as a climate refuge. Additionally, this population constitutes a unique natural heritage site that should be effectively protected from physical impacts and other direct consequences of anthropogenic activities.