Abstract In ensemble Kalman filter (EnKF) data assimilation, localization modifies the error covariance matrices to suppress the influence of distant observations, removing spurious long-distance correlations. In addition to allowing efficient parallel implementation, this takes advantage of the atmosphere’s lower dimensionality in local regions. There are two primary methods for localization. In B localization, the background error covariance matrix elements are reduced by a Schur product so that correlations between grid points that are far apart are removed. In R localization, the observation error covariance matrix is multiplied by a distance-dependent function, so that far away observations are considered to have infinite error. Successful numerical weather prediction depends upon well-balanced initial conditions to avoid spurious propagation of inertial-gravity waves. Previous studies note that B localization can disrupt the relationship between the height gradient and the wind speed of the analysis increments, resulting in an analysis that can be significantly ageostrophic. This study begins with a comparison of the accuracy and geostrophic balance of EnKF analyses using no localization, B localization, and R localization with simple one-dimensional balanced waves derived from the shallow-water equations, indicating that the optimal length scale for R localization is shorter than for B localization, and that for the same length scale R localization is more balanced. The comparison of localization techniques is then expanded to the Simplified Parameterizations, Primitive Equation Dynamics (SPEEDY) global atmospheric model. Here, natural imbalance of the slow manifold must be contrasted with undesired imbalance introduced by data assimilation. Performance of the two techniques is comparable, also with a shorter optimal localization distance for R localization than for B localization.