Since underground structures in the sea area are difficult to observe, they are not well examined. To estimate underground structures beneath Seafloor Observation Network for Earthquakes and Tsunamis along the Japan Trench (S-net), which was installed in the sea area between the Japanese islands and the outer rise of the Japan Trench, horizontal-to-vertical spectral ratios of earthquake motions (EHVRs) recorded at S-net sites were calculated, and the EHVRs were inverted to obtain one-dimensional seismic velocity structures. The effect of reflected waves from sea surface was not found on the observed EHVRs; however, the sharp trough and directional dependency, possibly owing to the seismometers’ installing situation, were found on the observed EHVRs. Inversion analysis of the observed EHVRs based on the diffuse field concept for earthquake was performed within 0.1–3.0 Hz avoiding the sharp trough and the directional dependency. The observed EHVRs were well reproduced by the resultant seismic velocity structures. The travel times for S- and P-waves from the seismic bedrock (S-wave velocity =3100 m/s) to the seafloor were calculated from the identified structures, and it was distributed between 2.8 s and 3.8 s for S-wave velocity and 0.9 s and 1.3 s for P-wave velocity. Comparing the identified structures with previous studies revealed similar depths to seismic bedrock; however, some discrepancies were noted. Such correspondences and discrepancies exhibit the validity and limitation of our inversion models. The possible causes of discrepancies are the difference of the observed data, the target frequency range, and the inversion conditions. Therefore, in the future, more detailed investigations should be performed.

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