Many previous studies have revealed distribution of strain rates in the Japanese Islands using data of continuous GNSS station installed since mid 1990’s. They discovered “strain concentration zones” including the Niigata-Kobe Tectonic Zone and the Ou backbone Range in inland and a side of Sea of Japan away from major plate boundaries including the Nankai Trough and Japan Trench. We used GNSS data after the increase of GNSS stations in 2002 and examined distribution of site velocities and strain rates during 2005-2009 with higher spatial resolution. And then, we compared it with major active faults and found that many active faults locate in regions where maximum shear strain rates were high. We also removed elastic deformation due to interplate coupling on the subducting plate interface along the Nankai Trough and compared between distribution of the corrected strain rates and shallow seismicity. The comparison suggests a tendency that the higher maximum shear strain rates, the more frequent shallow M >_ 6 earthquakes occur. We, therefore, suggest that the GNSS data is incorporated into long-term evaluation of large inland earthquakes.