A semiconductor device and a manufacturing method thereof are provided which can suppress corrosion by chemicals in processes, while preventing generation of thermal stress on a mark. A semiconductor device includes a semiconductor layer with a front-side main surface and a back-side main surface opposed to the front-side main surface, a plurality of light receiving elements formed in the semiconductor layer for performing photoelectric conversion, a light receiving lens disposed above the back-side main surface for supplying light to the light receiving element, and a mark formed inside the semiconductor layer. The mark extends from the front-side main surface to the back-side main surface. The mark has a deeply located surface recessed toward the front-side main surface rather than the back-side main surface. The deeply located surface is formed of silicon.