A six month herpetological survey was undertaken between March and September 2015 on Nosy Komba, an island off of the north-west coast of mainland Madagascar which has undergone considerable anthropogenic modification. A total of 14 species were found that have not been previously recorded on Nosy Komba, bringing the total island diversity to 52 (41 reptiles and 11 frogs). The species assemblage, richness and abundance of four distinct habitat types were compared: closed-canopy forest, disturbed-canopy forest, shade-grown coffee plantation and mixed open plantation. The anthropogenic habitats on Nosy Komba were found to be of high conservation value for reptile species, where species richness and abundance found during surveys was equal to or higher than closed-canopy forest. By contrast, the abundance and species richness for frogs was reduced in anthropogenic habitats, especially in sun-exposed plantations. The forested areas of Nosy Komba contain twelve IUCN threatened species (9 reptiles and 3 frogs). Of these, Uroplatus henkeli, Uroplatus ebenaui, Phelsuma seippi, Zonosaurus subuniclor, Stumpffia psologlossa and Stumpffia pygmaea were also found in shade-grown coffee plantations, demonstrating the conservation value of these anthropogenic environments. Five threatened species on Nosy Komba were found exclusively in forested areas: Brookesia minima, Brookesia ebenaui, Lygodactylus madagascariensis, Rhombophryne testudo and Thamnosophis stumpffi. Our surveys demonstrate the importance of Nosy Komba for conserving regionally endemic and threatened species, and the often under-appreciated value of anthropogenic environments in species conservation, when also coupled with the protection of primary forest.