According to one embodiment, a method of manufacturing a magnetic recording medium comprises forming a protective film on a ferromagnetic recording layer containing Cobalt (Co) on a substrate and forming a recess in both the protective film and the ferromagnetic recording layer at a part where a nonmagnetic layer is to be formed. The method further comprises removing Co from a part of the recess of the ferromagnetic recording layer to form the nonmagnetic layer that separates magnetic patterns made of the ferromagnetic recording layer containing Co. The nonmagnetic layer has an identical chemical composition as the ferromagnetic recording layer, except for the nonmagnetic layer having a lower Co concentration than the magnetic patterns.