AbstractCuba, the largest island in the Greater Antilles, hosts a high diversity of native squamate reptiles and is characterized by a complex geological history. The island has undergone repeated submergence and emergence, positioned on the dynamic border between the Caribbean and North American tectonic plates. Here, we infer current areas of endemism on Cuba based on squamate distributions using standard parsimony analysis of endemism under the “areas of endemism as individuals” hypothesis. We diagnose 29 areas of endemism, 14 of which are nested within other areas of endemism, from 52 squamate taxa. We suspect the current biotic pattern is a composite view of layered histories, and we summarize the geological history of the island to contemplate historical periods that left stronger marks on squamate distributions than others.