Although the terrestrial herpetofauna of the Bahamas Archipelago is largely well characterized, many smaller or outlying islands and island banks are poorly studied owing to their remoteness. The Cay Sal Bank is an uninhabited island bank lying between the Florida Keys and western Cuba. Politically a part of the Commonwealth of the Bahamas, the Cay Sal islands are disjunct from the rest of the Bahamas Archipelago to the east. The bank supports 117 small emergent islands around its perimeter, on which at least six species of squamates have been recorded. Recent expeditions have added to this species list, although several islands remain unsurveyed. Of these six squamate species, only Anolis fairchildi is considered endemic to the bank. The evolutionary relationships of the other species are speculated to derive from either Bahamian or Cuban progenitors. Here we report on a recent expedition to the Cay Sal Bank, and provide updated and novel island records. We further characterize the two native Anolis species and one Tropidophis species using molecular phylogenetic analyses to estimate the likely origins and divergence times of these species. We find that both Anolis species are recently (< 2 Mya) derived from, and likely conspecific with, west Cuban ancestors, whereas the Tropidophis is likely conspecific with the populations of Tropidophis curtus on the Great Bahamas Bank. Thus the terrestrial squamate herpetofauna on the bank are a product of dispersal from both the Great Bahamas Bank to the east and western Cuba to the south. We provide an updated understanding of the biogeography and evolutionary history of these squamates on the Cay Sal Bank.