Dwarf mistletoes (Arceuthobium spp., Viscaceae) are ecologically and economically important parasitic flowering plants. Despite detection of morphological and host specialization differences, ribosomal DNA and plastid sequence information have not resolved genetic differentiation among the dwarf mistletoes parasitizing white pines (Pinus subgenus Strobus) in the western U. S. A. We assessed the effectiveness of integrating amplified fragment length polymorphism and morphometric analyses in the delineation of three closely related and morphologically similar species of white pine dwarf mistletoes. Using amplified fragment length polymorphism data for 995 loci, we quantified intra- and inter-specific genetic variation, tested for geographic isolation-by-distance, and visualized genetic patterns using Bayesian-based structure analyses, neighbor-joining tree reconstruction, and principal coordinate analysis ordination. A total of 19 morphological characters were also analyzed using standard statistical methods and discriminant analysis. We found that 13% of the total genetic variation (p = 0.0001) was due to among-species differences, and species were distinguished by tree and ordination plots. Species also differed in estimates of genetic diversity and differentiation, and the degree of isolation-by-distance in genetic structuring. Amplified fragment length polymorphism and morphometric analyses both demonstrated that the dwarf mistletoes examined are well-differentiated genetically and morphologically, and therefore, should be considered distinct species.