In a method of manufacturing a semiconductor device, an isolation layer pattern is formed on a substrate to define a field region covered by the isolation layer pattern and first and second active regions that is not covered by the isolation layer pattern and protrudes from the isolation layer pattern. A first anti-reflective layer is formed on the isolation layer pattern. A first photoresist layer is formed on the first and second active regions of the substrate and the first anti-reflective layer. The first photoresist layer is partially etched to form a first photoresist pattern covering the first active region. Impurities are implanted into the second active region to form a first impurity region.