A method of manufacturing semiconductor devices includes providing a semiconductor substrate including first active areas and isolation areas alternately arranged to be parallel to each other and second active areas connecting the first active areas to each other. A tunnel insulating layer, a charge storage layer, and an isolation mask are formed on the semiconductor substrate. The isolation mask, the charge storage layer, the tunnel insulating layer, and the semiconductor substrate are etched to form a trench on the isolation area. An isolation structure is formed on the trench. A dielectric layer, a conductive layer for a control gate, and a hard mask are sequentially formed on a structure that includes the isolation structure. The hard mask, the conductive layer for the control gate, the dielectric layer, and the charge storage layer are patterned to form drain select lines, word lines and source select lines intersecting the first active area. Junction areas are formed on the first active areas through an ion implanting process. A common source is formed on the first active areas and the second active area between adjacent source select lines.