Systems and methods for alien wavelength management. One embodiment is an apparatus for managing alien wavelengths for a Wavelength Division Multiplexing (WDM) system. The apparatus includes memory to store signal thresholds for alien wavelength signals transmitting over the WDM system, wherein the alien wavelength signals are generated by third-party equipment independently controlled from the WDM system. The apparatus also includes an Alien Wavelength Control Unit (AWCU) coupled between the third-party equipment and a channelization port of the WDM system, the AWCU configured to measure a signal parameter of an alien wavelength signal transmitted by the third-party equipment to the channelization port. The apparatus further includes a controller coupled with the AWCU and configured, in response to determining that the signal parameter is outside a signal threshold of the WDM system, to direct the AWCU to modify the alien wavelength signal to protect the WDM system.