Madagascar is home to 400 species of reptiles, 69 of which can be found at Ambatovy i.e. 16% of the reptile species in the country. To preserve its biodiversity-rich intervention areas, Ambatovy has implemented specific environmental management programs, which include a program on the preservation of three reptile species inventoried in the International Union for Conservation of Nature (IUCN) Red List of threatened species. They are two species of geckos, Phelsuma pronki (diurnal) and Uroplatus pietschmanni (nocturnal) and one species of the world’s smallest chameleon, Brookesia ramanantsoai. Manual salvaging is used to help them migrate from the clearing area to the conservation zones, and Ambatovy thoroughly monitors their adaptation to their new habitat.

Like the other forest areas in Madagascar, Ambatovy shelters varied and diverse reptile species, which are for the most part endemic. These include tree snakes («fandrefiala», Ithycyphus perineti), terrestrial snakes (Menarana, Leioheterodon madagascariensis), geckos (tanafisaka, Uroplatus sikorae), chameleons of different sizes (Ramilaheloka small, Brookesia thieli), and aquatic turtles (Sokadrano, Pelusios subniger).