The taxonomic status of the geographically isolated population of Short-toed Snake-eagle Circaetus gallicus on the Lesser Sundas (=Nusa Tenggara) has been controversial. In the past they have been regarded as either a migrant population or a recently arrived resident population. Here we obtained DNA sequences from the mitochondrial cytochrome-b gene and combined genetic data with assessments of published and novel morphological data to clarify the taxonomic status of the Lesser Sundas population of C. gallicus. The cytochrome-b distance between the Lesser Sundas and Palearctic populations of C. gallicus is consistent with subspecific differentiation, indicating a possible divergence during one of the most recent Pleistocene glaciations. Although some of the morphological distinctions show overlap, the new subspecies can generally be diagnosed from nominate C. gallicus gallicus by being smaller and paler, and exhibiting less spotting and barring. Unlike nominate populations from mainland Eurasia, the new subspecies seems to lack pronounced sexual dimorphism. We here describe this new subspecies to science and discuss its biology and conservation status.