A method of manufacturing a semiconductor device includes forming device isolation layer in a substrate to define active regions of which each has first regions and a second region between the first regions, forming a first trench and a pair of second trenches in the substrate, and forming gates in the second trenches, respectively. The first trench extends in a first direction and crosses the active regions and the device isolation layer. The second trenches are connected to a bottom of the first trench and extend in the first direction at both sides of the second regions.