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We propose a semiblind channel-estimation method for multiple-input multiple-output (MIMO) single carrier with frequency-domain equalization systems. By taking advantage of periodic precoding and the block circulant channel model after cyclic prefix removal, we obtain the channel-product matrices by solving a series of decoupled linear systems, which is gained from the covariance matrix of the received data. Then, the channel-impulse-response matrix is obtained by computing the positive eigenvalues and eigenvectors of a Hermitian matrix formed from the channel-product matrices. We also propose an optimal design of the precoding sequence, which minimizes the noise effect and numerical error in covariance matrix estimation, and discuss the impact of the optimal sequence on channel equalization. With the proposed framework, the method is shown to be robust with respect to channel-order overestimation, and the identifiability condition is simply that the channel-impulse-response matrix has full column rank. Due to the identifiability condition, the method is applicable to MIMO channels with more transmitters or more receivers. Simulations are used to demonstrate the performance of the proposed method.