Probabilistic linear discriminant analysis (PLDA) has been widely used in open-set verification tasks, such as speaker verification. A potential issue of this model is that the training set often contains limited number of classes, which makes the estimation for the between-class variance unreliable. This unreliable estimation often leads to degraded generalization. In this paper, we present an MAP estimation for the between-class variance, by employing an Inverse-Wishart prior. A key problem is that with hierarchical models such as PLDA, the prior is placed on the variance of class means while the likelihood is based on class members, which makes the posterior inference intractable. We derive a simple MAP estimation for such a model, and test it in both PLDA scoring and length normalization. In both cases, the MAP-based estimation delivers interesting performance improvement.