The present invention relates to a method of forming a nanogap, a method of manufacturing a nano field effect transistor for a molecular device or a bio-sensor, and a fabrication thereof, and more particularly, to a method of forming a high reproductive nanogap using a thin layer with a molecular size or a size which is similar to that of a molecule and a nano field effect transistor manufactured by the method of forming the nanogap. The method of forming a nanogap according to the present invention comprises steps of (a) forming sequentially an insulating layer, a first metal layer and a hard mask on a silicon substrate; (b) etching partially the first metal layer using the mask as an etching mask; (c) forming a self-assembled monolayer (SAM) on a side surface of the first metal layer to form a nanogap on the silicon substrate; (d) depositing metal on the entire structure including the mask to form a second metal layer; (e) removing the metal deposited on the hard mask using a lift-off process by etching the mask formed in step (a) and (f) etching the SAM formed in step (c) to form the nanogap.