This invention is to provide a nanodevice, which is combined with an electronic device such as a diode, tunnel device and MOS transistor, integrated circuit and manufacturing method of the nanodevice. A nanodevice includes: a first insulating layer 2; one electrode 5A and the other electrode 5B provided to have a nanogap on the first insulating layer 2; a metal nanoparticle or a functional molecule provided between the one electrode 5A and the other electrode 5B; a second insulating layer 8 provided on the first insulating layer 2, and on the one electrode 5A and the other electrode 5B to embed the metal nanoparticle or the functional molecule. The second insulating layer works as a passivating layer.