We studied the mitochondrial DNA (mtDNA) haplotypes of Japanese macaques on Yakushima Island, Kyushu, Japan, using fecal DNA samples. The age-class of the macaques was estimated by measuring the size of feces from macaques from Arashiyama, Kyoto, and Yakushima. We observed at least four different mtDNA haplotypes from Yakushima: Yakushima 1 (n=34), Yakushima 2 (n=2), Yakushima 3 (n=2), and Yakushima 4 (n=1) (DDBJ; Accession No.: AB093529-32). The estimated size of the feces of juvenile macaques was <18mm and that of adolescent and adult macaques was >25mm at both Arashiyama and Yakushima. The results imply that analysis of mtDNA haplotypes in combination with age-class estimation through fecal measurements is a useful tool for studying matrilineal group structure and male dispersal patterns in the Yakushima macaques.