There are provided a semiconductor device which can be miniaturized without being deteriorated in characteristics, and a manufacturing method thereof. The semiconductor device includes a semiconductor substrate having a main surface, a source region and a drain region formed apart from each other in the main surface, a gate electrode layer formed over the main surface sandwiched between the source region and the drain region, a first conductive layer formed so as to be in contact with the surface of the source region, and a second conductive layer formed so as to be in contact with the surface of the drain region. A recess is formed in the main surface so as to extend from the contact region between the first conductive layer and the source region through a part underlying the gate electrode layer to the contact region between the second conductive layer and the drain region.