The unique butterfly species, Baronia brevicornis, perhaps the oldest taxon in the Papilionidae, is known to have a very restricted distribution in Mexico. Populations are restricted to southern Mexico in deciduous scrub forest where its host-plants, Acacia trees (Leguminosae), are common and widespread. Little is known of the conservation implications of its relationship with its host trees. We recorded fine scale population data for larval and adult B. brevicornis in 22 km2 of fragmented landscape in southern Mexico. Habitat associations determined from over 1319 transect walks reveal that B. brevicornis exhibited an extremely localised distribution, occupying < 1% of the study area and being mostly associated with Acacia woodlots. Detailed analyses of habitat requirements for larva and/or adult B. brevicornis suggest that it lays its eggs on Acacia pennatula and A. macracantha (two newly recorded larval host-plants), that eggs were laid disproportionately on Acacia trees with long branches (χ2 = 17.7, P < 0.001) and that the probability of finding adult B. brevicornis between occupied and un-occupied Acacia woodlots increased with host-plant density (χ2 = 18.4, P < 0.001). The results of this study suggest that conservation recommendations for B. brevicornis must consider the condition of the Acacia habitat network, given that Acacia is mostly associated with human-managed grazing systems. Effective conservation will require the establishment of connected networks of patches where natural dynamics can produce new habitats, as well as the creation of new habitats within colonisation distance. This research provides a rare case study of conservation biology of a Neotropical insect, emphasising the importance of using ecological information to provide management recommendations.