Madagascar is renowned for its impressive species richness and high level of endemism, which led to the island being recognized as one of the world’s most important biodiversity hotspots. As in many other regions, Madagascar’s biodiversity is highly threatened by unsustainable anthropogenic disturbance, leading to widespread habitat loss and degradation. Although the country has significantly expanded its network of protected areas (PAs), current protocols for identifying priority areas are based on traditional measures that could fail to ensure maximal inclusion of the country’s biodiversity. In this study, we use Madagascar’s largest endemic plant family, Sarcolaenaceae, as a model to identify areas with high diversity and to explore the potential conservation importance of these areas. Using phylogenetic information and species distribution data, we employ three metrics to study geographic patterns of diversity: species richness, Phylogenetic Diversity (PD) and Mean Phylogenetic Diversity (MPD). The distributions of species richness and PD show considerable spatial congruence, with the highest values found in a narrow localized region in the central-northern portion of the eastern humid forest. MPD is comparatively uniform spatially, suggesting that the balanced nature of the phylogenetic tree plays a role in the observed congruence between PD and species richness. The current network of PAs includes a large part of the family’s biodiversity, and three PAs (Ankeniheny Zahamena Forest Corridor, the Bongolava Forest Corridor and the Itremo Massif) together contain almost 85 % of the PD. Our results suggest that PD could be a valuable source of complementary information for determining the contribution of Madagascar’s existing network of PAs toward protecting the country’s biodiversity and for identifying priority areas for the establishment of new parks and reserves.