The genus Polygala (Polygalaceae) contains ca. 600 species that are distributed worldwide. A recent taxonomic evaluation of Polygala in Madagascar recognized 19 species in the island, as well as two new species from Toliara Province. The first new species from the area around Saint Augustin, Polygala labatii, is only known from two collections and belongs to the endemic P. sect. Madecassa. The second new species, Polygala mandrarensis, is distributed in the region of the Mandrare River basin and belongs to P. sect. Tetrasepalae. In this work, we describe and illustrate these two new species of Polygala. We also provide a key to the infrageneric taxa of Polygala in Madagascar, as well as keys to P. sect. Madecassa and the Malagasy species of P. sect. Tetrasepalae, and present a distribution map and make preliminary conservation assessments using IUCN Red List categories and criteria.