A semiconductor device including: a semiconductor substrate including an active region; a plurality of conductive structures formed over the semiconductor substrate; an isolation layer filling a space between the conductive structures and having an opening that exposes the active region between the conductive structures; a pad formed in a bottom portion of the opening and in contact with the active region; a plug liner formed conformally over a sidewall of the opening and exposing the pad; and a contact plug formed over the pad inside the opening.