A multi-junction photodiode for molecular detection and discrimination and fabrication methods thereof. The multi junction photodiode includes a substrate having first conductive type dopants, an epitaxial layer having the first conductive type dopants, a deep well having second conductive type dopants, a first well having the first conductive type dopants, a second well having the second conductive type dopants, a third well having the first conductive type dopants, and a first doped region having the second conductive type dopants. The epitaxial layer is disposed on the substrate. The deep well is disposed in the epitaxial layer. The first well having three sides connected to the epitaxial layer is disposed in the deep well. The second well is disposed in the first well. The third well having three sides connected to the epitaxial layer is disposed in the second well. The first doped region is disposed in the third well.