The study of population genetics attempts to investigate evolutionary forces such as mutation, migration, genetic drift, selection and recombination, and how gene frequencies change in populations to shape their genetic structure. These evolutionary forces and the interaction among them are particularly important in plant pathogens where, combined with the pathogen’s life history characteristics, they determine the pathogen’s evolutionary potential. Advances in DNA sequencing and analytical approaches have significantly improved the accuracy of population genetic parameter estimates. In particular, coalescent-based approaches are a powerful extension of classical population genetics because it is a collection of mathematical models that can accommodate biological phenomena as reflected in molecular data. In a comparison of migration estimates of Rhynchosporium secalis, which were either derived from F_ST estimates, or estimated with a coalescent method, reveals that the latter are more reliable, are less dependent on population sizes being stable, are not affected by asymmetrical migration between populations, and are affected less by populations with small sample sizes. Improved analyses and their usefulness in determining the phylogeography and demography of R. secalis are discussed.