Methods of fabricating a gate-insulating layer of a dual-gate semiconductor device are disclosed. A disclosed method comprises sequentially forming a buffer oxide layer and a nitride layer on a semiconductor substrate having at least one high voltage device area and at least one low voltage device area; forming at least one trench by selectively removing at least one portion of the buffer oxide layer, the nitride layer and the semiconductor substrate; forming at least one device isolation layer by depositing an oxide layer in the trench and planarizing the oxide layer; removing the nitride layer and the buffer oxide layer remaining on the high voltage device area; forming a first gate-insulating layer on the high voltage device area; removing the nitride layer and the buffer oxide layer remaining on the low voltage device area; and forming a second gate-insulating layer on the low voltage device area.