In this study, we analyze the ground motion characteristics of October 20, 2006 Manyas (M-L=5.2) and October 24, 2006 Gemlik (M-L=5.2) earthquakes. Both earthquakes occurred on the southern branch of the North Anatolian Fault Zone in Marmara region, which has a lower seismic hazard relative to the northern branch. The two events are the largest earthquakes on the southern branch recorded by a modern and vast seismological network; therefore their records are valuable to evaluate seismic risk of the region and the understanding of physics of wave propagation. The analysis show that the attenuation of PGAs is very similar for two earthquakes, but they are not represented by the empirical relation obtained for earthquakes occurred on the northern branch. The waveforms of the Gemlik earthquake recorded by BYT-Net array indicate an EW rupture orientation with right-lateral slip which fits to the general character of the southern branch. Ground motions at the stations located within basin are strongly influenced by the presence of locally induced surface waves resulting in lengthening of significant shaking duration with respect to a nearby ridge site. Surface wave characteristics are very similar for the Manyas and Gemlik earthquakes, but variations are observed on components which may be related to 3D basin geometry. Resonance frequencies of the surface waves generated within basin are very close to the 1D site resonances at the stations obtained from H/V ratios of S waves. The resonance frequency is about 0.2 Hz within the large Bursa Plain, whereas it increases to about 0.9 Hz within the smaller Gemlik Plain.