Belize has long been considered a leader in conservation within the Mesoamerican region with 36% of its terrestrial area under protection status. However, a gap analysis conducted in 2005 reveal savannas are under-represented by the existing network of protected areas. With the savannas under numerous threats which include climate change, infrastructure development, deforestation and species decline, it has become necessary to address the current protected area effectiveness for the savanna regions. MARXAN software was used to identify the state of the current protected areas within savannas and identify regions that may be critical for future conservation. Various boundary length modifiers and species penalty factors were tested in a selection of species target scenarios. A final portfolio based on seeded and locked versions of MARXAN scenarios were used to identify priority conservation areas with high biodiversity and high vulnerability. Combined conservation values were assigned to selected regions based on the irreplaceability index, species richness, and human footprint costs. These areas have the potential to guide future planning and decision making for protected area conservation in savanna ecosystems in Belize.