In a method of fabricating a flash memory device, trenches are formed in an isolation area of a semiconductor substrate. A first insulating layer is formed on sidewalls and bottoms of the trenches. Conductive layer patterns are formed on the first insulating layers at the bottoms of the trenches. A second insulating layer is formed on the conductive layer patterns. Gate lines are formed over a semiconductor substrate including the second insulating layer. The gate lines intersect the conductive layer patterns. Junctions are formed on the semiconductor substrate between the gate lines. An interlayer insulating layer is formed over the semiconductor substrate including the gate lines. Contact holes are formed through which the conductive layer patterns and the junctions located on one side of the conductive layer patterns are exposed. The contact holes are gap-filled with a conductive material, thereby forming contact plugs.