Provided is a manufacturing method of a semiconductor device, which comprises forming a film stack of a gate insulating film, a charge storage film, insulating film, polysilicon film, silicon oxide film, silicon nitride film and cap insulating film over a semiconductor substrate; removing the film stack by photolithography and etching from a low breakdown voltage MISFET formation region and a high breakdown voltage MISFET formation region; forming gate insulating films, polysilicon film and cap insulating film over the semiconductor substrate, forming a gate electrode in the low breakdown voltage MISFET formation region and high breakdown voltage MISFET formation region, and then forming a gate electrode in a memory cell formation region. By the manufacturing technology of a semiconductor device for forming the gate electrodes of a first MISFET and a second MISFET in different steps, the present invention makes it possible to provide the first MISFET and the second MISFET each having improved reliability.