Effective representation of all species in local conservation planning is a major challenge, particularly in poorly known but highly fragmented biological ‘hotspots’. Based on 105 months of studies over 49 years, we reviewed the status of 915 species and 910 subspecies of butterflies known in the Philippines. We identified 133 globally threatened and conservation-dependent endemic Philippine taxa. The current system of 18 priority protected areas provides at least one protected area for 65 of these but no areas for 29 species and 39 subspecies. Of the 133 taxa, 71% do not have a stable population inside a priority site. A total of 29 taxa is endangered or critically endangered; 83% of these do not occur within a priority site. Least protected are the lowland taxa. The minimum network required to include each threatened and conservation-dependent taxon of butterfly within at least one area would comprise 29 sites. The Sulus and Mindanao hold disproportionate numbers of threatened butterflies. Our findings suggest limited cross-taxon congruence in complementarity-derived priority sets. A large proportion of the priority areas for Philippine butterflies do not coincide with known priority areas for mammals and birds. We demonstrate that a better resolved species level classification could reveal numerous ‘new’ priority areas. In tropical island and mountain regions where the distinctiveness of butterfly subspecies is high, significant evolutionary units may be lost unless fine-scale conservation planning pays attention to well-defined subspecies.