Abstract A series of specimens of an unidentified species of the genus Lygodactylus from Fernando de Noronha Island were found in the herpetological collections of the Museu Nacional, Rio de Janeiro (Brazil). No species of this genus were known to occur in the archipelago. A review of the historical reports regarding the herpetofauna of the island failed to provide evidence regarding the presence of the species in the last centuries. Morphological comparisons with the two other species of the genus occurring in South America, L. klugei and L. wetzeli, allowed us to confidently confirm that the Fernando de Noronha population belonged to a putatively new species. Here we describe this population as a new species and discuss its possible extinction causes in the archipelago. We also debate the importance of historical natural history collections to the study of biodiversity.