A Mw 6.1 earthquake occurred on April 1st, 2006 near Taitung, eastern Taiwan. It produced significant coseismic ground displacements and a large number of aftershocks in the ensuing month. This event provides an opportunity to diagnose the seismogenic structure in the southern Longitudinal Valley (LV) of eastern Taiwan, long viewed as one of the collision sutures between the Philippine Sea and the Eurasian plates. With precisely relocated main- and aftershock hypocenters, focal mechanisms for M ≥ 3.8 events, and coseismic ground displacements from strong motion records, we determine a main shock dislocation model. Our results indicate that the main shock occurred on a high angle fault (azimuth 198¿, dip 77¿). The model comprises a fault with two segments; the main shock and a large number of aftershocks are associated with the northern segment that exhibited predominantly left-lateral strike-slip motion, in agreement with P-wave first motions and waveform (USGS) solutions. The southern segment exhibits a slightly larger thrust component, in agreement with CMT solutions. Tectonically, this event highlights a NNE-trending fault on the west side of the LV, which is predominantly strike-slip. The aftershocks clustered to the east of the main shock, which exhibit mainly thrust mechanisms, indicate that shortening is still acting on the sedimentary materials deposited between the Coastal and Central ranges prior to collision. As a result, the southern LV is undergoing slip partitioning along different faults, which has never been specified before.