Puerto Rico is a highly seismically active island, where several damaging historical earthquakes have occurred and frequent small events persist. It situates at the boundary between the Caribbean and North American plates, featuring a complex fault system. Here, we investigate the seismotectonic crustal structure of the island by interpreting the 3D compressional‐wave velocity VP and compressional‐ to shear‐wave velocity ratio VP/VS models and by analyzing the distribution of the relocated earthquakes. The 3D velocity models are obtained by applying the simul2000 tomographic inversion algorithm based on the phase arrivals recorded by the Puerto Rico seismic network. We find high‐VP and low‐VP/VS anomalies in the eastern and central province between the Great Northern Puerto Rico fault zone and the Great Southern Puerto Rico fault zone, correlating with the Utuado pluton. Further, there are low‐VP anomalies beneath both the Great Southern Puerto Rico fault zone and the South Lajas fault, indicating northerly dipping structures from the southwest to the northwest of the island. We relocate 19,095 earthquakes from May 2017 to April 2021 using the new 3D velocity model and waveform cross‐correlation data. The relocated seismicity shows trends along the Investigator fault, the Ponce faults, the Guayanilla rift, and the Punta Montalva fault. The majority of the 2019–2021 Southwestern Puerto Rico earthquakes are associated with the Punta Montalva fault. Earthquakes forming 17° northward‐dipping structures at various depths possibly manifest continuation of the Muertos trough, along which the Caribbean plate is being subducted beneath the Puerto Rico microplate. Our results show complex fault geometries of a diffuse fault network, suggesting possible subduction process accommodated by faults within a low‐velocity zone.

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