AbstractWe present a full‐waveform tomographic model of the crust and upper mantle beneath the Japanese Islands region. This is based on the combination of GPU‐accelerated spectral‐element wavefield simulations, adjoint techniques, and nonlinear optimization. Our model explains complete seismic waveforms of events not used in the inversion in the period range from 20 to 80 s. Quantitative resolution analysis indicates that resolution lengths within the well‐covered areas are around 150 km in the horizontal and around 30 km in the vertical directions. In addition to the high‐velocity signatures of known lithospheric slabs in the region, our model reveals a pronounced low‐velocity anomaly beneath the volcanic island of Ulleung in the Sea of Japan, reaching −19% around 100 km depth. The Ulleung anomaly originates at or above the Pacific slab, rises vertically upward to the base of the Philippine Sea slab at ∼200 km depth, circumvents it in NW direction, and then significantly strengthens in the uppermost mantle above the Philippine Sea slab. Among the numerous hypotheses for the generation of low‐velocity anomalies in subduction systems, those invoking instabilities before or when a slab enters the transition zone seem most likely. The age and fast subduction of the Pacific slab may facilitate the transport of fluids into the transition zone. This may promote the reduction in viscosity and the onset of convective upwelling, aided by ambient mantle flow, such as return flow within the mantle wedge.