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Time and wavelength division multiplexed passive optical network (TWDM-PON) is one of the most promising candidates of the next generation optical access system beyond 10Gb/s. The TWDM-PON system stacks multiple 10Gigabit PONs (XG-PONs) by employing tunable transmitters and tunable receivers at ONUs. In the TWDM-PON media access control (MAC) layer, wavelength management becomes a critical issue of resource sharing and assignment. In this paper, we propose a mechanism to manage multiple wavelengths in the TWDM-PON system. We also model this problem by using multiprocessor scheduling analysis. Two types of heuristic algorithms have been proposed to relax the NP-hard complexity problem and promote online implementation. A TWDM-PON prototype system has been built to evaluate its performance. The proposed two algorithms have been implemented in the prototype system to test their wavelength tuning cost and load balancing capability. Analysis and test demonstrate salient results. To the authors' best knowledge, this is the first work of implementing the multiple wavelength management mechanism in an actual TWDM-PON prototype system, and the reported results in this paper benefit the ongoing next generation passive optical network stage 2 (NG-PON2) research and standards efforts.