Amplified restriction fragment polymorphism (AFLP) technique was used to examine the putative hybrid populations between Aconitum japonicum ssp. napiforme and A. jaluense ssp. jaluense, which was suggested by morphological features. The majority of Mt. Bagoon populations were genetically clustered with A. japonicum ssp. napifome, but Mt. Chiri populations were clustered with A. jaluense ssp. jaluense. One individual of Mt. Bagoon polulation was clustered with Mt. Chiri populations. Molecular genetic data suggest that these populations are of hybrid origin between A. japonicum ssp. napiforme and A. jaluense ssp. jaluense and that hybrids have repeatedly undergone backcrosses to either of parental species.