Methods of manufacturing a semiconductor device are provided. The method includes forming a poly-silicon layer doped with first p-type dopants on a substrate, etching the poly-silicon layer and the substrate to form a poly-silicon pattern and a trench, forming device isolation pattern covering a lower sidewall of the poly-silicon pattern in the trench, thermally treating the poly-silicon pattern in a gas including second p-type dopants, forming a dielectric layer and a conductive layer on the thermally treated poly-silicon pattern and the device isolation pattern, etching the conductive layer, the dielectric layer, and the thermally treated poly-silicon pattern to form a control gate, a dielectric pattern, and a floating gate respectively.