One of Brazil's most threatened tropical biome is the Atlantic Forest. This biome has distinct forest formations, as the Araucaria Mixed Forest, a sub-tropical ecosystem distributed through southern and southeastern Brazil, surrounded by Dense Ombrophilous Forest. The defining tree species of Araucaria Mixed Forest is Araucaria angustifolia (known as Araucaria), an endangered, relict, and historically managed conifer. Due to unsustainable exploitation during the twentieth century, the main strategy for Araucaria preservation was the creation of protected areas. However, protected areas' coverage within Atlantic Forest remains scarce and might not prevent connectivity between species' remnant patches. We thus evaluated the potential connectivity of projected Araucaria distribution in the present and future under climate change and current land-use, using a species distribution model with graph theory. Araucaria's current connectivity—through the Mixed and Dense Forests—ranges entirely through the landscape, with 715 connecting arcs (212 within protected areas). However, only 7% of its current distribution is encompassed by protected areas. Under future climate change in 2085, connectivity is expected to decrease by 77% compared with current projections. In the future, Araucaria subpopulations will be concentrated at higher elevations in unprotected suitable areas. We suggest that specific regions in southern and southeastern Brazil might be targeted as priority conservation areas jointly to major existing protected areas. These areas will sustain Araucaria connectivity and protection. As a keystone species, by safeguarding Araucaria we protect the socioecological system in southern and southeast Brazil and potentially promote forest expansion.