The study reported on the first molecular estimates of phylogenetic relationships of Brachymeles dalawangdaliri (Scincidae) and Pseudogekko isapa (Gekkonidae), and present new data on phenotypic variation in these two poorly known taxa, endemic to the Romblon Island Group of the central Philippines. Furthermore, the work emphasizes the conservation significance of Sibuyan Island’s Mt. Guiting-Guiting Natural Park, the diverse, idiosyncratic biogeographic histories of its variably-assembled, highly endemic reptile fauna, and the critical importance of multiple, repeated, survey–resurvey studies for understanding forest community species composition and the evolutionary history of Philippine biodiversity.