Marine infrastructures are generally vulnerable to strong seismic waves propagating through their seabed foundation. However, only limited attentions have been given to the dynamic seabed response around marine structures under strong seismic loading in the past, although numerous cases of failure of marine infrastructures during strong earthquake events have been reported in the literature. In this study, employing the dynamic Biot's equation as the governing equation, in which the accelerations of both soil and pore water are considered, a three-dimensional (3D) FEM soil model for consolidation and dynamic analysis is developed. With the proposed model, the dynamic response of a rubble mound breakwater and its porous seabed foundation under the seismic wave recorded in the Japan 311 off the pacific coast of Tohoku earthquake (M magnitude=9.0) is investigated. Numerical results indicate that the rubble mound breakwater vibrates strongly in the earthquake process. The porous seabed foundation amplifies the seismic wave significantly from the bottom to the surface.