Pinus monticola (Dougl. ex D. Don.) maintains a complex defence system that detects white pine blister rust pathogen (Cronartium ribicola J.C.Fisch.) and activates resistance responses. A thorough understanding of how it functions at the molecular level would provide us new strategies for creating forest trees with durable disease resistance. Our research focuses on molecular dissection of P. monticola major gene (Cr2) resistance and quantitative partial resistance. To characterize the Cr2 gene, resistance gene family encoding proteins with nucleotide-binding-site and leucine- rich- repeat (NBS-LRR) was identified and used to search for DNA polymorphisms by genotyping with a modified approach of amplified fragment length polymorphism (AFLP).