A method of fabricating a nonvolatile memory device includes preparing a semiconductor substrate including a cell array region. The method also includes forming a recessed region in the cell array region by etching the semiconductor substrate. The method includes etching at least a portion of the semiconductor substrate that partially includes the recessed region and forming first and second trenches that differ in depth, intersect the recessed region, and link with each other. The method includes forming a device isolation layer having rugged bottoms and defining an active region by filling an insulating material in the first and second trenches. The method includes forming a gate insulation layer on the semiconductor substrate of the active region including the recessed region and forming a gate structure on the gate insulation layer, to fill the recessed region, the gate structure including a floating gate, an intergate insulating pattern, and a control gate.