We review a model-based approach to estimate local population FST’s that is based on the multinomial-Dirichlet distribution, the so-called F-model. As opposed to the standard method of estimating a single FST value, this approach takes into account the fact that in most if not all realistic situations, local populations differ in their effective sizes and migration rates. Therefore, the use of this approach can help better describe the genetic structure of populations. Despite this obvious advantage, this method has remained largely underutilized by molecular ecologists. Thus, the objective of this review is to foster its use for studying the genetic structure of metapopulations. We present the derivation of the Bayesian formulation for the estimation of population-specific FST’s based on the multinomial-Dirichlet distribution. We describe several recent applications of the F-model and present the results of a small simulation study that explains how the F-model can help better describe the genetic structure of populations.