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This paper presents a novel joint channel and physical layer network decoding scheme for a two-way relay communication system. The proposed decoding scheme can be viewed as a serial concatenated decoding scheme with the source codes, different or identical, as the outer codes and the physical network coding (PNC) as the inner code. To achieve good error performance, iteratively decodable codes are used as the source codes. Decoding of the scheme consists of two loops, the inner-loop for which the source codes are decoded with a message-passing decoding algorithm and the outer-loop for which the reliability messages are passed between the source decoders and the PNC decoder for updating message reliabilities. Using two different protograph repeat-accumulate codes as the source codes for low decoder complexity, the proposed scheme achieves a superior performance. In the case that the source codes are identical, the proposed scheme outperforms the previously proposed decoding schemes for two-way relay communication systems with two source nodes.