In this paper, we discuss the relationship between the accurate hypocentral distribution and three-dimensional (3-D) geological structure in and around the Horonobe area in northern Hokkaido, Japan. The multiplet-clustering analysis was applied to the 421 micro-earthquakes which occurred from 1 September, 2003 to 30 September, 2007. The 3-D geological structure model was mainly constructed from previous seismic reflection profiles and borehole data. As a result of this analysis, although with slight differences in depth between them, the hypocenters were found to be distributed in the NNW-SSE direction and become deeper from the west toward the east. The distributed pattern of the hypocenters is similar to that of the geological structure. These results indicate that the hypocentral distribution may represent existence of active zone related to the geological structure, and provide effective information which can contribute to establishing methods for estimating the future evolution of the geological environment.