We call the realized variance (RV) calculated with observed prices contaminated by microstructure noises (MNs) the noise-contaminated RV (NCRV) and refer to the component in the NCRV associated with the MNs as the MN component. This paper develops a method for estimating the integrated variance (IV) and MN component simultaneously, extending the state space method proposed by Barndorff-Nielsen and Shephard (2002). Our extension is based on the result obtained in Meddahi (2003), namely, when the true log-price process follows a general class of continuous-time stochastic volatility (SV) models, the IV follows an ARMA process. We represent the NCRV by a state space form and show that the state space form parameters are not identifiable; however, they can be expressed as functions of fewer identifiable parameters. We illustrate how to estimate these parameters. The proposed method is applied to yen/dollar exchange rate data. We find that the magnitude of the MN component is, on average, about 21%-48 % of the NCRV, depending on the sampling frequency.