A semiconductor device includes a memory section formed at a semiconductor substrate and including a first transistor having an ONO film that can store charges between the semiconductor substrate and a memory electrode and a first STI region for isolating the first transistor, and a CMOS section formed at the semiconductor substrate and including a second transistor having a CMOS electrode and a gate dielectric and a second STI region for isolating the second transistor. The height of the top surface of the first STI region is set equal to or smaller than the height of the top surface of the second STI region.