Genetic relationships were examined among specimens of a subspecies of the Japanese common charr, Salvelinus leucomaenis imbrius (Gogi), distributed around the watershed boundaries in the western Chugoku Mountains on the basis of Random Amplified Polymorphic DNA (RAPD) analysis. A total of 23 fish was collected from 16 branches of 4 rivers. Twenty-one DNA fragments were amplified, among which there were no bands common only to all the individuals of a branch or a river system. A genetical identity was observed among the branches of the two facing river systems across a watershed, the Takatsu and Nishiki River systems. The highest two average Band Sharing Index (BSI) values were also observed between these river systems. Average BSI was the lowest between the Nishiki and Ohta River systems, although their rivermouths are adjacent. BSI between the individuals showed a significantly negative relationship against the distance between the collection sites. Two large clusters comprised the individuals from 3 or all the river systems at BSI level of 0.8. Some intimate clusters were constructed by the facing branches of different river systems. These results suggest that the genetic distance of the Gogi might be strongly determined not by the river system but by the geographical closeness.