The 2019 MJ 6.7 Yamagata-Oki earthquake occurred adjacent to the northeastern edge of the source region of the 1964 MJ 7.5 Niigata earthquake, offshore of Yamagata Prefecture, Japan. Few aftershocks occurred in the source region of the Yamagata-Oki earthquake immediately following the Niigata earthquake, and the recent seismicity rate in this region is low compared with the source region of the Niigata earthquake. This spatial variation in seismicity may allow us to elucidate plausible physical processes that shape the spatiotemporal evolution of these shallow-crustal environments. Here, we investigate the spatial variations in seismicity characteristics by applying the HIerarchical Space–Time Epidemic Type Aftershock Sequence (HIST-ETAS) model to an earthquake catalog compiled by the Japan Meteorological Agency for events in and around the Yamagata-Oki earthquake rupture region. We compare spatial variations in the background seismicity rate and aftershock productivity estimated from the HIST-ETAS model with the geophysical features in the study region. The background seismicity rate is high along the eastern margin of the Sea of Japan and correlates well with a previously identified zone that possesses a high geodetic E-W strain rate. The two major earthquakes occurred in and around a high E-W strain rate zone, suggesting that the background seismicity rate may serve as a key parameter for evaluating seismic hazard across the Japanese Archipelago. Furthermore, the source region of the Yamagata-Oki earthquake has a higher aftershock productivity, lower e-value, and lower seismic-wave velocity than that of the Niigata earthquake. We interpret this low-velocity zone to be a well-developed damaged rock that resulted in both a reduction in the b-value and an increase in aftershock productivity based on previous laboratory experiments and numerical results; this damage makes the rock more ductile at the macroscopic scale. The higher ductility in the source region of the Yamagata-Oki earthquake may have worked as a barrier against the propagation of dynamic rupture that occurred during the Niigata earthquake.