The sarus crane (Grus antigone) ranges across two continents and is the only species of crane (Gruidae) that breeds in India and Southeast Asia. Four subspecies, the Indian sarus (G. a. antigone), the eastern sarus (G. a. sharpii), the Australian sarus (G. a. gillae) and the extinct Philippine sarus (G. a. luzonica) were originally described through morphological, plumage, and/or geographical differences. The ranges of the Indian and eastern sarus converge in eastern India and Myanmar, but the Australian sarus has a disjunct Australian distribution. This study assesses population genetic structure of the current sarus populations utilising 13 DNA microsatellite loci. Population structure within this species was investigated utilising traditional FST and Bayesian clustering methods. While significant divergence was observed among populations when individuals were assigned to geographical populations, analyses based solely on individual genotypes demonstrated a clinal nature to the variation. The results of this study suggest that the Indian and eastern sarus cranes represent two major breeding groups within Asia and that the birds from Myanmar probably reside in an introgression zone between them. Lastly, because of genetic similarities shown to the eastern sarus, the results support recent theories contending that the Australian sarus was derived from mainland Asian birds.