Subspecies are often less well-defined than species but have become one of the basic units for legal protection. Evidence for the erection or synonymy of subspecies therefore needs to be founded on the best science available. Here we show that there is clear genetic disjunction in the Sarus Crane Antigone antigone, where previously the variation had appeared to be clinal. Based on a total sample of 76 individuals, analysis of 10 microsatellite loci from 67 samples and 49 sequences from the mitochondrial control region, this research establishes that the Australian Sarus Crane A. a. gillae differs significantly from both A. a. antigone (South Asia) and A. a. sharpii (Myanmar and Indochina). A single sample from the extinct Philippine subspecies A. a luzonica clustered with A. a. gillae, hinting at the potential for a more recent separation between them than from A. a. antigone and A. a. sharpii, even though A. a. sharpii is closer geographically. The results demonstrate that failure to detect subspecies through initial genetic profiling does not mean discontinuities are absent and has significance for other cases where subspecies are dismissed based on partial genetic evidence. It could also be potentially important for sourcing birds for reintroduction to the Philippines.