A method of manufacturing a flash memory device is characterized by preventing photoresist patterns from being formed directly on or removed directly from a surface of the substrate or the dielectric layer. This is accomplished by separately forming a control gate layer of transistors in a cell area of the substrate and a gate layer of transistors in a peripheral circuit area of the substrate. The method of the present invention includes the steps of forming in a peripheral circuit area of the substrate a gate insulating layer for both high and low voltage regions of the peripheral circuit area and then forming the gate conduction layer on the gate insulating layer. The method of the present invention further comprises the steps of forming in a cell area of the substrate a transistor structure composed of a tunneling gate insulating layer, a floating gate layer, a dielectric layer, and a control gate layer.