Based on phylogenetic and morphological evidence, we describe a new species of Cyrtodactylus from Obi Island in the northern Moluccas, Indonesia. The new species is genetically and morphologically allied to the Melanesian species Cyrtodactylus papuensis but is distinguished by its larger body size, fewer midbody scale rows, deep precloacal groove in males, and enlarged nonpored femoral scales and pored precloacal scales arranged in a continuous series. The new species is also genetically divergent from C. papuensis (p-distances of 19.0%–20.1% in the mitochondrial NADH dehydrogenase subunit 2 gene). Four species of Cyrtodactylus are now known from the northern Moluccas, but it is likely additional species remain unrecognized.