Entire nucleotide sequence of the mitochondrial control region was obtained for the red-crowned crane Grus japonensis and two closely related species, the common crane G. grus and the hooded crane G. monacha. Control regions of these crane species could be divided into three subdomains (I, II, III) by incidence of sequence variation. The central domain II was well conserved with C, D and F sequence motifs, while both flanking domains were variable, with greater base substitution in 5′ domain I than 3′ domain III with CSB-1 motif. In addition, a 51 base-pair (bp) sequence was found to be deleted in the 5′ portion of domain I in G. grus and G. monacha compared with the domain I sequence of G. japonensis. Comparison of 418 bp sequence in variable 5′ portion spanning domain I and 5′ part of domain II among 29 individuals of G. japonensis including 14 from the East Asia mainland population and 15 from the Japan's endangered Hokkaido island population revealed seven haplotypes in the former and only two haplotypes in the latter. Small number of haplotypes in the Hokkaido population suggested less genetic variation than in the mainland population, possibly reflecting a “bottleneck” effect. Although the two studied populations shared no common haplotypes, they are likely to belong to a common lineage because of no independent branch of each population on the parsimony network and neighbor-joining tree.