In a method of manufacturing a semiconductor device including a planar type transistor and a fin type transistor, a substrate having a first region and a second region is partially to form an isolation trench defining an isolation region and an active region. An insulation layer liner is formed on sidewalls of the isolation trench in the first region and the second region. An isolation layer fills an inner portion of the isolation trench. The insulation layer liner is partially removed to expose an upper surface of the substrate in the gate region of the first region, and an upper surface and sidewalls of the substrate in the gate region of the second region. A gate oxide layer and a gate electrode are formed on the exposed substrate.