Earthquakes with small magnitude and shallow depths are one form of manifestation of existence a fault line in Yogyakarta. Accurate hypocenter determination is needed to identify tectonic and fault conditions based on earthquake hypocenter distribution recorded by seismograf. Hypocenter was determined by using two methods Geiger’s Adaptive Damping for early hypocenter and Modified Joint Hypocenter Determination (MJHD) for relocate hypocenter, we used 2 weeks aftershock data after main quake occurred on June 10-14 2006 with total of 625 events earthquake obtained from the results of picking waves. The difference of hyposenter result on the longitude and latitude is about 2 -25 km and depth change around 0.3-5 km with major distribution to the east from the fault. The final result of this relocation shows that the area is more easily releases energy is in the eastern section of the fault consisting of sedimentary rocks.