An integrative analysis of genetic, morphological, and ecological data recovered a new granite cave-adapted species, Cyrtodactylus raglaisp. nov., from the Song Giang River Valley, Khanh Hoa Province, Vietnam. Cyrtodactylus raglaisp. nov. is nested within one of two major clades within the irregularis species group where it forms a monophyletic group with C. cryptus and its sister species C. kingsadai. It differs from its sister species by an uncorrected pairwise sequence divergence of 16.5% and 16.8% based on the mitochondrial genes NADH dehydrogenase subunit 2 and its flanking tRNAs and the first subunit of cytochrome oxidase c (CO1), respectively. Cyrtodactylus raglaisp. nov. is a narrow-range endemic restricted to a riparian, granite cave microhabitat and its overall morphology bears that of other granite cave-dwelling ecomorphs in the genus. The Song Giang River Valley and its associated waterways are currently threatened by the construction of a hydropower station which will negatively impact the surrounding ecosystem. Urgent field surveys in this region are necessary in order to obtain critical data on its biodiversity and importance to conservation efforts in southern Vietnam.