A novel chokecherry genetic linkage map was constructed using 565 molecular markers and a previously published mapping population (n=101). Chokecherry (Prunus virginiana L.) is a potential model for genetic research of phytoplasmic diseases because of its natural resistance to X-disease (Candidatus Phytoplasma pruni). The novel chokecherry map was developed using JoinMap 4.0 and contains a complete set of 16 linkage groups. In total, the map spans a genetic distance of 2,172 cM with an average marker density of 3.97 cM. Three significant quantitative trait loci (QTL) associated with X-disease resistance were identified on linkage groups 15, 5, and 4 contributing to a total of 45.9% of the phenotypic variation. This novel genetic linkage map and the identified QTL linked to X-disease resistance will provide the framework needed to facilitate molecular genetics, genomics, and breeding research concerning X-disease in chokecherry and other Prunus species.