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The M 7.8 Kaikoura earthquake occurred in the northern South Island of New Zealand on 3 Nov., 2016, involving the rupture of >20 faults. To understand the complexity of the Kaikoura earthquake, details of the fault ge- ometry, seismic velocity distribution, and stress field are necessary. We have undertaken seismic tomography along the c. 200 km length of the rupture zone. Data from both 51 temporary stations and 22 permanent (GeoNet) stations were collected from March 2011 to December 2018. The hypocenter of the Kaikoura earthquake and aftershocks near the Kekerengu fault locate along lineaments where seismic velocity changes laterally in the epicentral region. In the uppermost crust, lower velocities occur beneath the Emu Plain and Cape Campbell. A higher velocity region near Kaikoura may have acted as a barrier that prevented eastward rupture from the hypocenter and led to the complex fault distribution in this area. These complexities in the seismic velocity structure may relate to the multi-segment rupture character of the Kaikoura earthquake. Spatial correlations between rupture areas and high Vp/Vs suggest the involvement of overpressured fluid in the nucleation and propagation of rupture segments, which is also supported by the reactivation of unfavourably oriented strike-slip ruptures, many lying at c.70◦ to the regional maximum compressive stress trajectories.