A coupled ensemble square root filter–three-dimensional ensemble-variational hybrid (EnSRF–En3DVar) data assimilation (DA) system is developed for the operational Rapid Refresh (RAP) forecasting system. The En3DVar hybrid system employs the extended control variable method, and is built on the NCEP operational gridpoint statistical interpolation (GSI) three-dimensional variational data assimilation (3DVar) framework. It is coupled with an EnSRF system for RAP, which provides ensemble perturbations. Recursive filters (RF) are used to localize ensemble covariance in both horizontal and vertical within the En3DVar. The coupled En3DVar hybrid system is evaluated with 3-h cycles over a 9-day period with active convection. All conventional observations used by operational RAP are included. The En3DVar hybrid system is run at ? of the operational RAP horizontal resolution or about 40-km grid spacing, and its performance is compared to parallel GSI 3DVar and EnSRF runs using the same datasets and resolution. Short-term forecasts initialized from the 3-hourly analyses are verified against sounding and surface observations. When using equally weighted static and ensemble background error covariances and 40 ensemble members, the En3DVar hybrid system outperforms the corresponding GSI 3DVar and EnSRF. When the recursive filter coefficients are tuned to achieve a similar height-dependent localization as in the EnSRF, the En3DVar results using pure ensemble covariance are close to EnSRF. Two-way coupling between EnSRF and En3DVar did not produce noticeable improvement over one-way coupling. Downscaled precipitation forecast skill on the 13-km RAP grid from the En3DVar hybrid is better than those from GSI 3DVar analyses.