A method of manufacturing a super-junction semiconductor device facilitates increasing the epitaxial growth rate without increasing the manufacturing steps greatly. In substitution for the formation of alignment mark in the surfaces of the second and subsequent non-doped epitaxial layers, patterning for forming a new alignment mark is conducted simultaneously with the resist pattering for selective ion-implantation into the second and subsequent non-doped epitaxial layers in order to form the new alignment mark at a position different from the position, at which the initial alignment mark is formed, and to form the new alignment mark in every one or more repeated epitaxial layer growth cycles.