Disclosed is a semiconductor device having an align key and a method of fabricating the same. The semiconductor device includes a semiconductor substrate having a cell area and an align key area. An isolation layer that defines a cell active area is disposed in the cell area of the semiconductor substrate. A cell charge storage layer pattern is disposed across the cell active area. An align charge storage layer pattern is disposed in the align key area of the semiconductor substrate. An align trench self-aligned with the align charge storage layer pattern is formed in the align key area of the semiconductor substrate.