In this article, a shear plate was mounted on the bottom in a wave flume and direct measurements of the smooth and rough bed shear stress under regular and irregular waves were conducted with the horizontal force exerted on the shear plates by the bottom shear stress in the wave boundary layer. Under immobile bed condition, grains of sand were glued uniformly and tightly onto the shear plate, being prevented from motion with the fluid flow and generation of sand ripples. The distribution of the bottom mean shear stress varying with time was measured by examining the interaction between the shear plate and shear transducers. The relation between the force measured by the shear transducers and its voltage is a linear one. Simultaneous measurements of the bottom velocity were carried out by an Acoustic Doppler Velocimeter (ADV), while the whole process was completely controlled by computers, bottom shear stress and velocity were synchronously measured. Based on the experimental results, it can be concluded that (1) the friction coefficient groews considerably with the increase of the Reynolds number, (2) the shear stress is a function varying with time and linearly proportional to the velocity. Compared with theoretical results and previous experimental data, it is shown that the experimental method is feasible and effective, A further study on the bed shear stress under regular or irregular waves can be carried out. And applicability to the laboratory studies on the initiation of sediments and the measurement of the shear stress after sediment imigration.