I describe a new species of frog of the Hylarana signata species complex from Mt. Busa, Sarangani and South Cotobato provinces, southern Mindanao Island, Philippines. The new species is distinguished from all other members of the H. signata complex by a unique combination of characters of external morphology, biochemical allelic variation, and the species’ position in phylogeny, estimated by analysis of multilocus DNA sequence data. Justification for recognition of the new species is further supported by marked sequence divergence in mitochondrial and nuclear genes. The new species has been collected only once in >20 yr despite targeted survey efforts on Mindanao, and multiple possible explanations are available to explain its extreme rarity. The recognition of this species, on the basis of a single previously misidentified specimen, accentuates the importance of collecting large sample sizes of specimens during faunistic surveys. Recognition of a new species from a locality that has now been heavily disturbed by commercial logging also emphasizes the extreme conservation importance of the last remaining forest fragments in the southern Philippines.