Widespread and poorly studied species complexes confound phylogenetic understanding of the Old World terrestrial orchid genus Nervilia. Recent taxonomic studies have suggested greater species richness in Asia than previously envisaged.We used morphological, cytological, and molecular phylogenetic analyses to confirm the existence of a novel, cryptic species of the Nervilia adolphi-punctata species alliance in southwest Japan, supporting earlier findings from a genetic fingerprinting study. Nervilia futago is formally described and illustrated here. In the vegetative state, the new species is practically inseparable from the more widespread N. nipponica, with which it co-occurs at several sites, but it can be distinguished in flower by its glabrous petals, by the lack of tall clavate hairs on the lip, and by the placement of the pollinia on the stigma prior to anthesis. Chromosome numbers and DNA content also differ. Despite their wide geographic separation, sequence data indicate greater affinity of N. futago to Himalayan members of the alliance than to other species of East Asia. The utility of genetic approaches in resolving identities and relationships in this taxonomically intractable genus is emphasised.