Disclosed is a method and an apparatus for selecting a wavelength in a hybrid Passive Optical Network (PON) system. The method of selecting a wavelength by a wavelength selecting apparatus in a hybrid passive optical network system includes: performing synchronization with any one of a plurality of downstream wavelengths; when the synchronization is succeeded, determining whether to select the synchronized downstream wavelength for a registration to an optical line terminal; and when it is determined to select the synchronized downstream wavelength, performing the registration to the optical line terminal through the synchronized downstream wavelength.