This Special Issue is devoted to the study of caves and other subterranean sites with 25 or more specialized species (stygobionts and troglobionts), in a geological and hydrogeological context. These investigations, including those in the previous Special Issue, deal with 26 of the 30 known sites. These hotspots are widely distributed in temperate and subtropical zones, but are few in the tropics. A concentration of hotspots can be found in southern Europe. Contrastingly, no known hotspots have been located in Africa.