Due to common interference or noise propagation, noise correlation between relays could occur in Amplify-and-Forward relay networks. To estimate channel coefficient, the noise covariance is required in traditional channel estimations. On the other hand, we also need channel coefficient to estimate the noise covariance. Therefore,traditional channel estimators can not be utilized when noise correlation is unknown. In this paper, we propose an Expectation-Maximization algorithm based iterative channel estimator to solve this problem. Moreover, we analyze the modified Cram'er-Rao bound to show the performance of the proposed channel estimation. Finally, simulation results show that the proposed channel estimator can work well in Amplify-and- Forward relay networks with unknown noise correlation.