To improve a semiconductor device having a nonvolatile memory. a first MISFET, a second MISFET, and a memory cell are formed, and a stopper film made of a silicon oxide film is formed thereover. Then, over the stopper film, a stress application film made of a silicon nitride film is formed, and the stress application film over the second MISFET and the memory cell is removed. Thereafter, heat treatment is performed to apply a stress to the first MISFET. Thus, a SMT is not applied to each of elements, but is applied selectively. This can reduce the degree of degradation of the second MISFET due to H (hydrogen) in the silicon nitride film forming the stress application film. This can also reduce the degree of degradation of the characteristics of the memory cell due to the H (hydrogen) in the silicon nitride film forming the stress application film.