The third largest Biodiversity Hotspot of the world, Mesoamerican forests are declining due to human pressures. Based on species distribution models calibrated for 1224 native tree species in Mesoamerica, we identified high-value forest conservation areas at the resolution of a 10 km × 10 km cells using the Zonation Reserve Selection software, and investigated whether these high-value forest conservation areas are well represented by the World Database on Protected Areas network. We had three key findings. First, dry forest is the least protected biome in Mesoamerica (4.5% protected), indicating that further action to safeguard this biome is warranted. Secondly, the poor overlap between protected areas and high-value forest conservation areas found herein may provide evidence that the establishment of protected areas may not be fully accounting for tree priority rank map. Third, high percentages of forest cover and high-value forest conservation areas still need to be represented by the protected areas network. Because deforestation rates are still increasing in this region, Mesoamerica needs funding and coordinated action by policy makers, national and local governmental and non-governmental organizations, conservationists and other stakeholders.