A method of manufacturing a semiconductor device including forming an ONO film on a semiconductor substrate and a hard mask layer on the ONO film, forming a trench by etching the hard mask layer and the ONO film on a field region of the semiconductor substrate using a photo etch process and etching the field region of the semiconductor substrate, and forming a device separator at the trench. The method also includes exposing the ONO film by removing the hard mask layer on the ONO film, and leaving the ONO film only on a prospective SONOS gate in a cell region of the semiconductor substrate and removing the ONO film the remainder region thereof. The method further includes forming a gate oxide film on the semiconductor substrate at an outside of the ONO film, and forming a gate electrode on the gate oxide film and the ONO film, respectively.