A semiconductor device with a charge holding capacitor comprises a lower electrode connected via a plug to one of the source and drain of an MIS transistor, a capacitor insulating film formed the lower electrode, an upper electrode formed on the capacitor insulating film. The lower electrode includes a first constituting portion that is embedded in a hole in which the plug has been embedded and so formed that it self-aligns with the plug and a second constituting portion which is formed on the first constituting portion and on regions outside the fist constituting portion and whose cross section is larger than that of the first constituting portion. The first constituting portion and the second constituting portion are formed integrally by a continues film.