Inventories at Masoala National Park have revealed sixty-nine species of reptiles, including some species unique to the area. 

The chameleons are especially well known for three characteristics. First, chameleons are able to move their eyes independently to look in all directions without moving their heads! This very peculiar system of vision enables them to aim at their prey with precision. When a chameleon locates a tasty insect, it uses its very long tongue to capture it. The tongue can extend to be longer than the chameleon itself. Chameleons are perhaps best known for their ability to change color for camouflage, or as a means of communication during social exchanges (either confrontational or as mating displays).

Several snake species are also present at Masoala, but they do not pose a threat to people. One beautiful type of snake is the Malagasy tree boa, which chokes its prey.

The genus Phelsuma comprises the day geckos, the emblematic reptile species of Madagascar. The geckos are generally recognizable by their brilliant green colors and red spots.