We have identified “N”-shaped Y/X amplitude spectral ratios in S-coda records from a significant number of OBSs (ocean bottom seismometers) belonging to in-line-type ocean bottom networks of S-net and ETMC deployed around the Japan Trench and Sagami Trough, respectively. The “N”-shape reflects a sharp peak and notch at approximately 5–13 Hz and 10–23 Hz, respectively. This shape does not characterize OBSs belonging to node-type ocean bottom network of DONET deployed near the Nankai Trough. For S-net stations, the “N”-shape is not clearly formed for stations installed within grooves dug in the seafloor. We interpret the “N”-shaped Y/X amplitude spectral ratio is caused by the natural vibrations of a cylindrical pressure vessel that is placed sideways (long-axis lies in the horizontal plane) on the seafloor. The notch and peak frequencies in the Y/X amplitude spectral ratio likely correspond to natural frequencies of longitudinal (X-direction) and torsional and/or bending (Y-direction) vibrations, respectively. These natural vibrations are not observed for buried OBSs or those installed within grooves in the seafloor probably because they are better coupled to the seafloor. We propose a simple model to evaluate the extent to which the peak and notch have formed, which depends on the natural frequencies and coupling of the pressure vessel. We suggest users of in-line-type OBSs carefully examine if there are different responses between the X and Y components when frequencies about > 3 Hz are used. When installing OBS networks in the future, installing OBSs and cables within grooves dug in the seafloor or by burial will be effective in suppressing such natural vibrations.