In accordance with the teachings of the present invention, a system and method for managing communication in a hybrid passive optical network (HPON) is provided. In a particular embodiment, the method includes transmitting, at a first wavelength, a first configuration message on the HPON. The method also includes receiving at one or more of a plurality of receivers at an optical line terminal (OLT) one or more configuration response messages from one or more optical network units (ONUs) in a first set of ONUs. The method further includes, based on the configuration response messages from the first set of ONUs, associating, in a database, each ONU in the first set of ONUs with the first wavelength and with the receiver receiving the configuration response message from the ONU. The method also includes, after transmitting the first configuration message, transmitting, at a second wavelength, a second configuration message on the HPON. The method further includes receiving at one or more of the plurality of receivers at the OLT one or more configuration response messages from one or more ONUs in a second set of ONUs, wherein the ONUs in the second set of ONUs do not belong to the first set of ONUs. The method also includes, based on the configuration response messages from the second set of ONUs, associating, in the database, each ONU in the second set of ONUs with the second wavelength and with the receiver receiving the configuration response message from the ONU.