A method of manufacturing a semiconductor device includes forming first and second gate structures on a substrate in first and second regions, respectively, forming a first capping layer on the substrate by a first high density plasma process, such that the first capping layer covers the first and second gate structures except for sidewalls thereof, removing a portion of the first capping layer in the first region, removing an upper portion of the substrate in the first region using the first gate structure as an etching mask to form a first trench, and forming a first epitaxial layer to fill the first trench.