Manufacturing a laser diode includes growing an active layer, a first InP layer, and a diffraction grating layer; forming an alignment mark having a recess by etching the diffraction grating layer and the first InP layer; forming a first etching mask; forming a diffraction grating in the diffraction grating layer using the first etching mask; forming a modified layer containing InAsP on a surface of the alignment mark recess by supplying a first source gas containing As and a second source gas containing P; growing a second InP layer on the diffraction grating layer and on the alignment mark; forming a second etching mask on the second InP layer; selectively etching the second InP layer embedded in the recess of the alignment mark through the second etching mask by using the modified layer serving as an etching stopper; and forming a waveguide structure using the alignment mark.