Coneworms of the genus Dioryctria Zeller are important lepidopterous pests of conifer cones throughout the Holarctic region. Seventy-nine Dioryctria species are currently recognized and arranged into 11 species groups, but a globally unified classification of these species groups has not been attained. We surveyed 14 Dioryctria species belonging to 7 species groups recognized as being taxonomically problematic. Mitochondrial DNA sequences and morphological characters were used to resolve relationships among and within species groups and species. Sequences were obtained for 2.3 kb of the mitochondrial COI + COII genes and related to 52 morphological characters. Parsimony analyses of separate and combined data showed that (i) the five included Chinese species (D. abietella (Denis and Schiffermüller), D. rubella Hampson, D. nr. rubella, D. magnifica Munroe, and D. yiai Mutuura and Munroe) were distinct from the North American taxa, and their relationships were interspersed among Nearctic and European species; (ii) three of the four species groups represented by more than one species formed robust, well-supported clades (abietella group, sylvestrella group, and zimmermani group) for both mtDNA sequences and morphology; (iii) mtDNA and morphology gave conflicting interspecific and intergroup relationships for the auranticella, schuetzeella, ponderosae, and baumhoferi groups; (iv) all eight species for which more than one specimen was sampled were characterized by discrete clusters of mitochondrial DNA haplotypes, and mtDNA divergences among species in the same species group were generally less than those among species in different species groups; and (v) combining mtDNA data with morphological data increased support for most nodes in the phylogeny, with morphological characters providing support for species groups and mtDNA being essential for distinguishing species within species groups. This study demonstrates the value of a combined analysis of both mtDNA and morphological characters and establishes a phylogenetic framework for broader and more comprehensive studies of Dioryctria species.