The Atotsugawa fault system (AFS), characterized by high seismicity of micro-earthquakes, is an active zone of right-lateral strike-slip faults in central Japan. We carried out seismo-geological studies of three sites on the system. One is in the middle of the master Atotsugawa fault (AGF), one is at the end, and another is on a branching Mozumi-Sukenobe fault (MSF). Trenching surveys demonstrated a maximum recurrence interval of 3,000 years, which is similar to that of the central AGF (2,500 years). This might indicate a uniform behavior in the seismogenic zone, despite the apparent segmentation in the shallower AGF. Another geo-slicing survey at MSF depicted a scarce interval of 13,500 years, about six times longer than that of the master fault. Two simultaneous events on both AGF and MSF occurred in 1858 A.D. and at about 17,300 years ago, suggesting an intermittent cooperation between the master and branch faults of AFS.