We extract sequences of small repeating earthquakes to clarify inter-plate coupling of subducting plates over a large area of the Japanese Islands. As a result, many sequences are detected at the Philippine Sea plate subducting from the Ryukyu trench and Pacific plate subducting from the Kuril-Japan trench. The average slip-rates and standard deviations estimated from the sequences show substantial spatial changes of inter-plate coupling. The large deviations of slip-rates correspond to the occurrence of episodic slips such as after-slips following large earthquakes. Constant slip-rates approaching the relative plate motion indicate weak coupling areas. Slip deficits and sparse distributions of repeating groups suggest locked areas. In the Nankai trough, deep low-frequency earthquakes in the transition zone and burst-type repeating sequences within plates have not been located in the downdip direction of groups with slow slip-rates. This suggests that the space-time characteristics of inter-plate coupling affected these seismic events.