The generation and evolution of shedding vortices induced by a solitary wave propagating over a two-dimensional submerged obstacle, a rectangular dike or a vertical plate, was investigated experimentally. The vortex shedding process was observed qualitatively using laser induced fluorescence (LIF) technique and particle tracing technique. The velocity fields were measured quantitatively using particle image velocimetry (PIV). Base on the results of the flow visualization, the comparison of the vortex shedding processes between rectangular dike and vertical plate was qualitatively made under the same wave condition. It is noted that the process of either rectangular model or vertical plate can be divided into four common phases, but the characteristics of shedding vortices are different in the same phase. In addition, the velocity similarity profiles for the formation of separated shear layer and the formation of vertical jet were also quantitatively compared between rectangular dike and vertical plate.