Microtremor survey was conducted together with boring survey for the determination of site amplification and strong ground motion characteristics in southern Yogyakarta Depression, Indonesia. 1-D dynamic response analysis by equivalent linear method had been performed based on results of microtremors survey, data from nine boreholes, and standard penetration test results. The DYNEQ Program, version 3.25, coded by Dr. Nozomu Yoshida in 2004 was used for 1D dynamic response analysis by combining with Bunsanf – HV – Matsuo Program. 1-D seismic response analysis had been performed by using the input parameters such as shear wave velocity structures, sediment properties, depth information and two input earthquake motions at engineering bedrock; selected earthquake motion (2004 Kamo earthquake, Max Acc. 232 gals) and synthetic earthquake motion of 2006 Yogyakarta earthquake. The amplification map, two predominant period maps, two peak ground acceleration (PGA) maps, a peak ground velocity (PGV) map and a peak ground displacement (PGD) map are resulted as main contributions.