There is provided a method of manufacturing a light emitting diode, the method including: growing a first conductivity type nitride semiconductor layer and an active layer on a substrate in a first reaction chamber; transferring the substrate having the first conductivity type nitride semiconductor layer and the active layer grown thereon to a second reaction chamber; and growing a second conductivity type nitride semiconductor layer on the active layer in the second reaction chamber, wherein an atmosphere including a nitride source gas and a dopant source gas supplying a dopant to be included in the second conductivity type nitride semiconductor layer is created in an interior of the second reaction chamber prior to the transferring of the substrate to the second reaction chamber. This method improves a system's operational capability and productivity. In addition, the crystallinity and doping uniformity of semiconductor layers obtained by this method may be improved.