Madagascar is one of the most biodiverse countries in Africa, due to its level of endemism and species diversity. However, the pressure of human activities threatens the last patches of natural vegetation in the country and conservation decisions are undertaken with limited data availability. In this study, we use free online datasets to generate distribution models of 1539 endemic trees and prioritise for conservation and restoration considering threat, alongside conservation value and cost. Threats considered include illegal logging, forest degradation and agriculture or slash and burns activities. We found that the areas with the highest potential concentration of species are along the north and south-east of the country where more than 400 tree species can be found. Most scenarios identify a common conservation and restoration priority area along the north east of the country. Our findings guide managers, conservation organizations or governments in decisions about where to invest their limited conservation resources.