Abstract-In conventional two-phase channel estimation algorithms for dual-hop multiple-input multiple-output (MIMO) relay systems, the relay-destination channel estimated in the first phase is used for the source-relay channel estimation in the second phase. For these algorithms, the mismatch between the estimated and the true relay-destination channel affects the accuracy of the source-relay channel estimation. In this paper, we investigate the impact of such channel state information (CSI) mismatch on the performance of the two-phase channel estimation algorithm. By explicitly taking into account the CSI mismatch, we develop a robust algorithm to estimate the sourcerelay channel. Numerical examples demonstrate the improved performance of the proposed algorithm.