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Molecular genetics is proving to be especially useful for addressing a wide variety of research and management questions on the white pine blister rust pathosystem. White pine blister rust, caused by Cronartium ribicola, is an ideal model for studying biogeography, genetics, and evolution because: (1) it involves an introduced pathogen; (2) it includes multiple primary and alternate hosts occurring in large, relatively undisturbed ecosystems; (3) some hosts exhibit endemic resistance; and (4) the disease interaction is long enduring. Molecular techniques are used to investigate population genetics, phylogenetics, hybrids, and proteomics in white pine (Pinus, subgenus Strobus) and blister rust (Cronartium) and the genetics of resistance and virulence in the blister rust pathosystem. These techniques include genetic markers, mapping, microarrays, sequencing, association genetics, genomics, and genecology. Molecular genetics contributes to gene conservation, breeding for resistance, and ecosystem management.