Samples of the sika deer (Cervus nippon) were collected from Kyushu and Shikoku Islands of Japan and surrounding areas, and their nucleotide sequences were analyzed. Sequences of the whole control region of the mitochondrial DNA were determined and phylogenetic trees were constructed using the neighbor-joining method and the maximum likelihood method. We also investigated gene genealogies for the sequences using the statistical parsimony network approach. Phylogenetic trees showed that only the Yakushima/Tanegashima populations were genetically distant from other populations. The statistical parsimony network, however, indicated a close relationship of the Miyazaki populations to some of the Shikoku populations. It was suggested that Shikoku Island played an important role in the divergence from the southern Japan lineage of C. nippon.