The blue honeysuckle (Lonicera caerulea L.), a member of Caprifoliaceae family, is a circumholarctic shrub species with antioxidant-rich fruit. The potential health benefits of the fruit have motivated breeding efforts in Asia, Europe and North America. The University of Saskatchewan, Canada has one of the world’s most diverse blue honeysuckle germplasm collections, representing a broad range of environmental adaptation. This collection includes four known subspecies, an uncharacterized yet distinct phenotypic group and various types of inter-subspecific hybrids. To expand Canadian production of blue honeysuckle, in the temperate regions of coastal British Columbia, a core collection will be characterized for phenological, morphological and fruit quality traits. A set of 19 inter-simple sequence repeat (ISSR) oligonucleotide primers were used to amplify 319 polymorphic DNA fragments across thirty-two blue honeysuckle accessions to produce a genetic distance estimate. Cluster analysis (using the UPGMA method) produced a dendrogram with distinct clusters for the Japanese (subsp. emphyllocalyx), Eastern Canadian (subsp. villosa) and Russian accessions (subspp. edulis and kamtschatica) as well as an uncharacterized Kurile Island phenotype. Hybrid cultivars of Russian and Kurile pedigree were grouped in a separate cluster. These findings will be used to design breeding strategies to produce varieties with enhanced local adaptation for commercial-quality agronomic traits and high levels of antioxidants. The genetic markers will be used to confirm the identity of other types of inter-subspecific hybrids and to rapidly select appropriate germplasm accessions via molecular screening.