A phylogenetic analysis, based on the complete nucleotide sequences of the mitochondorial control region (D-loop), was conducted on Mola mola occurring around the Japan coast. Two significantly distant clades (bootstrap value 914, based on 1000 replicates) were recognized. One consisted of 19 specimens with 812-814 by D-loop sequences that were collected from geographically wide spread locations around Japan (Aomori to Kagoshima). The other clade consisted of 3 specimens (all greater than 2 m in total length) collected from the Pacific coast of eastern Japan and characterized by 817 by D-loop sequences with many nucleotide substitutions compared with the former clade (ca.100 positions).