A first MISFET which is a semiconductor element is formed on an SOI substrate. The SOI substrate includes a supporting substrate which is a base, BOX layer which is an insulating layer formed on a main surface (surface) of the supporting substrate, that is, a buried oxide film; and an SOI layer which is a semiconductor layer formed on the BOX layer. The first MISFET as a semiconductor element is formed to the SOI layer. In an isolation region, an isolation groove is formed penetrating though the SOI layer and the BOX layer so that a bottom surface of the groove is positioned in the middle of a thickness of the supporting substrate. An isolation film is buried in the isolation groove being formed. Then, an oxidation resistant film is interposed between the BOX layer and the isolation film.