The 2006 Yogyakarta earthquake struck the Indonesian island of Java with Mw 6.3 on May 26, 2006 that caused major damage and thousands of deaths in the area of Yogyakarta and Central Java province.Based on the aftershocks recorded by temporary seismic network deployed shortly after the earthquake disaster, the source of the 2006 earthquake was located about 20 km east of Opak fault. However, detail structure of 2006 earthquake's fault remains unclear. Its vicinity to highly populated Yogyakarta brings a reasonable motivation to investigate this geology structure and its potential hazard further. Until 2016, several weaker earthquakes were still felt by residents living around Opak fault and 2006 fault zone. To follow up this case, Gadjah Mada University and the Institut de Recherche pour le Developpement (IRD) conducted a seismic measurement around the faults area from October 2015 to May 2016. The purposes of this measurement were to determine the detail structure of the fault and to obtain velocity model of subsurface ( YOG ver 1.0) using Spatial Auto Correlation (SPAC) and Ambient Noise Tomography (ANT) method. Data acquisitions were carried out on the west side and the east side of the fault zone to map lateral velocity variation. Shear wave velocity, Vs contrast obtained by this measurement clearly indicates Opak Fault and 2006's fault zones which also reflects different types of lithology. This result improves the accuracy of local earthquake relocations and provides better images of local structures in Yogyakarta area. Through this research a processing software for Ambient Noise Tomography (GAMANT) also has been developed. As the measurement around Opak fault and 2006 fault zone shows very promising results, another experiment in Merapi will also be conducted this year to investigate the possible relation between crustal fault and volcanic activities.