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Two-way relaying systems are known to be capable of providing higher spectral efficiency compared with one-way relaying systems. However, the channel estimation problem for two-way relaying systems becomes more complicated. In this paper, we propose a superimposed channel training scheme for two-way MIMO relay communication systems, where the individual channel information for users-relay and relay-users links are estimated. The optimal structure of the source and relay training sequences are derived when the mean-squared error (MSE) of channel estimation is minimized. We also optimize the power allocation between the source and relay training sequences to improve the performance of the algorithm. Numerical examples are shown to demonstrate the performance of the proposed channel training algorithm.