Genetic diversity evaluation of Oriental white storks distributed in the Russian Far East was conducted based on D-loop haplotype data. In addition, to study the relationship between the wild Russian population and extinct Japanese populations, we compared the Russian haplotypes and reported Japanese haplotypes obtained from mounted specimens. The results showed that eight haplotypes with mutations at 18 sites were found in ten individuals. Two types of them were previously reported types and six haplotypes of them were previously unreported type. The haplotype diversity was 0.933. The average of pairwise difference among eight sequences was 0.007. Phylogenetic analysis suggested that there were three evolutionary lineages in the Russian population and the populations in the study area were genetically related to extinct Japanese population.