In this paper, we consider an identification problem for a system of partially observed linear stochastic differential equations. We present a result whereby one can determine all the system parameters including the covariance matrices of the noise processes. We formulate the original identification problem as a deterministic control problem and prove the equivalence of the two problems. The method of simulated annealing is used to develop a computational algorithm for identifying the unknown parameters from the available observation. The procedure is then illustrated by some examples.