Fish scale geckos (Geckolepis) are taxonomically poorly resolved, mainly because of the difficulty of applying standard morphological characters to diagnose taxa. Three species, Geckolepis maculata, G. polylepis, and G. typica, are currently recognized from Madagascar and the Comoro Islands. Molecular studies suggested a number of operational taxonomical units within the G. maculata complex, but none of these has been formally described. The Comoran population was described as Geckolepis humbloti Vaillant 1887 but later synonymized. Prior to our study, no genetic data and little other information were available for this taxon. We revised the status of G. humbloti using molecular genetics, external morphology, and osteological characters retrieved from 3D skeletal models created using micro-computed tomography (micro-CT). Our results demonstrate that G. humbloti represents a genetic lineage strongly distinct from all other Geckolepis species. It is furthermore distinguished by a combination of external morphological characters and probably by osteology. We therefore resurrect G. humbloti Vaillant, 1887 from synonymy with G. maculata. Remarkably, this lineage is not restricted to the Comoros: A specimen from Tsingy de Bemaraha in western Madagascar falls as a closely related sister lineage to all Comoran Geckolepis in our molecular phylogenetic analysis and is osteologically almost identical with a specimen from the type locality Grand Comoro. We therefore include it in G. humbloti. The phylogenetic topology and the intraspecific genetic divergences suggest that the Comoros were colonized naturally from western Madagascar by overseas dispersal. G. humbloti is not considered as threatened, but its presence is indicative of natural or near-natural habitats.