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Ammonia, as the reductant to convert NOx to nitrogen molecules in a selective catalytic reduction (SCR) catalyst, plays an important role in Diesel engine SCR control. To achieve a sophisticated SCR control, the presence of ammonia in the SCR should be precisely monitored. Ammonia sensor for gaseous concentration measurement has been available recently. However, ammonia can also be adsorbed on the SCR substrate which is unmeasurable but dominates the NOx reduction dynamics. And also the catalyst ammonia storage capacity serves as an important factor for the judgment of SCR catalyst aging. In this paper, an observer for SCR catalyst ammonia coverage ratio and storage capacity estimations is designed based on an extended Kalman filter (EKF). Simulation results verify that the EKF-based observer can estimate both the states well.