Sarus cranes (Grus antigone) are the tallest members of the crane family, Gruidae. They are found in four geographically distinct regions: northwest India (Indian Sarus- Grus antigone antigone), southeast Asia (Burmese Sarus- Grus antigone sharpei) and northern Australia (Australian Sarus- Grus antigone gillae). Although the three subspecies are morphologically distinct, their genetic distinctness is unclear. In this study, I focused on control region sequences of mitochondrial DNA (mtDNA) to assess the genetic and phylogeographic distinctness of Sarus subspecies. I used samples from four fragmented populations, seven from India, 16 from southeast Asia, five from Myanmar and eight from Australia. Phylogenetic trees were estimated using two Brolga crane sequences (G. rubicunda) as outgroups. All phylogenetic trees had low resolution, but AMOVA showed that all four Sarus populations are differentiated from each other. Nested clade phylogenetic analysis showed that most of the southeast Asian haplotypes are found at the center, suggesting that the Thai population includes the maximum number of ancestral haplotypes. Sarus cranes probably originated in southeast Asia and migrated both north towards India and south towards Australia during the last glacial maximum.