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This study examines the reflection of regular and irregular waves from a partially perforated caisson breakwater located on a step bed. The step bed is treated as an idealized rubble mound foundation. Based on the linear potential theory, an analytical solution is developed to calculate the reflection coefficient of the structure subjected to regular waves. The matched eigenfunction expansion method is used for the solution. The regular wave method is also extended to irregular waves using a linear transfer function. The calculated results obtained for limiting cases are exactly the same as corresponding results given by the previous researchers. The present predictions also agree well with experimental data in the published literatures. Numerical experiments are conducted to examine the variations of the reflection coefficient versus its main effect factors, and some interesting results are presented.