The Pamir and Hindu Kush are examples of a puzzling collision system where a complex junction of colliding lithospheric plates coexists with intermediate depth seismicity at 300 km. In this study, we constructed a new tomography model using travel time data from local events recorded by the TIPAGE (Tien Shan – Pamir Geodynamic program) network. In addition to the P- and S-wave velocities down to 200 km, we derived the azimuthal anisotropy. The velocity anomalies were consistent with the results of previous studies. In the crust, the velocity structure and anisotropy directions were mainly oriented along major suture zones. At depths of 80–120 km, a narrow low-velocity anomaly coinciding with the distribution of deep seismicity was interpreted as a trace of entrained crustal material by the dipping lithosphere. The anisotropy directions at these depths were mainly oriented northwest–southeast and were interpreted as indicating the direction of the motion of colliding plates. The difference in the magnitude of anisotropy south and north of the Pamir seismic zone suggests that the lithosphere coming from the south possesses less anisotropy than that of the Asian plate. The local tomography model was supplemented by previously computed regional tomography that expanded the area both laterally and axially. Beneath the Pamir, both continental plates coming from the north and south form a drop-shaped anomaly that will possibly delaminate in time. Beneath the Hindu Kush, we could clearly trace a continuous almost vertical subduction of the Katawaz block from the south. Thus, the continental collision beneath the Pamir and subduction beneath the Hindu Kush are separate processes with different rates and directions of plate movement.