During most of the past century, forest pathologists were limited to the study of pathogen phenotypes, vegetative compatibility, and mating reactions. These studies provided important insights in fungal taxonomy and phylogenetics, reproductive biology, and population genetics. However, these aspects are insufficiently variable or technically unfeasible for making inferences about intraspecific evolutionary processes (i.e., microevolution). Molecular techniques (Kim et. al., Chapter 2, this volume) and their application to population genetic analyses have given plant pathologists new tools that allow characterization of pathogens and their hosts at the species, population, and/or individual level. These data have enabled researchers to design experiments and test hypotheses on microevolutionary processes in situ. The outcome has been advancement in our basic understanding of organismal interactions from molecular processes to metapopulations and landscape effects.