The Java margin is part of the 5600 km long Sunda Arc subduction zone that extends from Sumatra to the Lesser Sunda Islands and is dominated by earthquakes with magnitude less than 7. Although several 7.0 ≤ Mw < 8.0 earthquakes have occurred, there has been an absence of Mw>8. Previous earthquake relocation studies have mainly focused on the ml ≥ 4 earthquakes, while seismic tomography studies have mainly focused on the volcanic system in Central and East Java. In this study, we aim to image the entirety of Java margin to investigate segmentation along this margin. We use the arrival time dataset from 2009 – 2018 collected from 44 stations in the BMKG national seismic network to relocate earthquakes and invert for seismic velocity structure along the Java margin using a finite-difference tomography algorithm. A total of 6041 earthquakes, 68250 P- and 22795 S-phases, ml 1.9 – 7.5, were included in the inversion, resulting in 4883 high-quality relocations. The distribution of relocated events shows several isolated clusters of seismicity at the trench, which are distributed nearly vertical, from the near-surface to 80 km depth. Feature with Vp/Vs ~ 1.73, which higher compared to value along the trench, coincides to one of the isolated clusters. Gaps are observed between bands of seismicity at the trench and beneath the forearc region. The seismicity is distributed surrounding or between the high anomalies of residual bathymetry which represent the structure of the subducting slab. Beneath the forearc, bands of seismicity are observed between 30 – 80 km depth and below 100 km depth. Their distribution reveals a steeper slab geometry relative to previously published slab models (Slab 1.0 and Slab 2.0). Several features with Vp/Vs < 1.70 and higher Vp and Vs than the surrounding area coincides with the bands of seismicity observed between 30 – 80 km depth. Shallow structure is also well defined by the earthquake relocations outlining three major faults (Cimandiri, Kencana-Rakutai faults, and an unnamed fault located east of Opak fault). The relocation results and velocity structure show that the distribution of seismicity along the subduction zone is segmented. This segmentation is likely related to the structure of the subducting plate.