The Mariana Trough is the youngest back-arc basin in a series of basins and arcs that developed behind the Mariana subduction zone in the western Pacific. Active seafloor spreading is ongoing at a spreading axis close the Mariana Arc resulting in a pronounced asymmetric configuration (double rate to the west 2:1) at 17° N. The formation of back-arc basins is controlled by the subducting slab, which regulates the temporal development of mantle flow, entrainment of fluids and hydrous melts together with the magma generation. To better understand the formation process of back-arc basins and the asymmetry of the central Mariana Trough, we combined 2-D P-wave traveltime tomography results together with high-resolution bathymetric data. Here, we show that the crust in the central Mariana Trough is 6.5-9.5 km thick, which is unusual for oceanic crust. The lower crust exhibits average seismic velocities of 6.5-7.2 km/s. High-velocity anomalies (7.4-7.9 km/s) in the lower crust at the margins of the Mariana Trough indicate that magmatic accretion process was affected by hydrous melting during rifting. While the Mariana Trough developed from a rather symmetric rifting (0.89:1) to a strongly asymmetric seafloor spreading stage (5.33:1), the contribution of hydrous melts declined and the opening direction changed. The asymmetric plate motions and the temporal change of the slab component influenced strongly the formation of the back-arc basin.