A semiconductor device includes a fin structure, first and second gate structures, a source/drain region, a source/drain contact layer and a separation layer. The fin structure protrudes from an isolation insulating layer disposed over a substrate and extends in a first direction. The first and second gate structures are formed over the fin structure and extend in a second direction crossing the first direction. The source/drain region is disposed between the first and second gate structures. The interlayer insulating layer is disposed over the fin structure, the first and second gate structures and the source/drain region. The first source/drain contact layer is disposed on the first source/drain region. The separation layer is disposed adjacent to the first source/drain contact layer. Ends of the first and second gate structures and an end of the source drain contact layer are in contact with a same face of the separation layer.