This paper presents the result of an archaeological study on the first prehistoric rock paintings site discovered in Madagascar and the wider Southwestern Indian Ocean basin. It provides archaeological evidence that contributes to the understanding of the prehistory of Madagascar as well as the distribution of African rock art. Until recently, Madagascar was not known to have prehistoric rock art. Through field survey conducted in 2010, rock paintings of red, claret, reddish orange, black, and white in monochrome, bichrome and polychrome styles were encountered in the Ampasimaiky rockshelter, in the Upper Onilahy, Southwestern Madagascar. Paintings were recorded, drawn, counted, and photographed for comparative analysis. Shape typology demonstrated naturalistic depictions of cattle, mainly of zebus, anthropomorphic stick figures, and Schematic-Geometric-Amorphous signs. The latter are dominated by quadrangular, circular and elliptical shapes, lines of dots/strokes, and alphabet-like signs. Through comparative study, a vertical set of geometric signs encountered at Ampasimaiky rockshelter has been identified as Libyco-Berber inscription. This would be the first evidence for early contact between Madagascar and Northern Africa during prehistoric times. Scanty materials such as potsherds and animal bones have been uncovered from the excavation of the shelter’s shallow deposits, but as yet no direct link has been established between this assemblage and the paintings. Even so, the presence of the Libyco-Berber inscription could be used to relatively date at least a part of the rock paintings to between 700 BC to roughly fifth century AD.