Manduca blackburni, commonly known as Blackburn’s Sphinx Moth, is a federally listed endangered species restricted to localized habitats on three islands in the Hawaiian archipelago. Manduca blackburni was thought to be closely related to the widely distributed New World species M. quinquemaculatus, but this has never been formally tested, and shortly after its description, many authors dismissed it as a subspecies or form of M. quinquemaculatus. We used one mitochondrial gene, COI, and two nuclear genes, CAD and EF-1α (2,975 bp total), to examine the phylogenetic relationships between M. blackburni and putative sister species in the genus. The phylogeny resulting from two single-gene analyses (CAD, COI) and the concatenation of all three genes suggest that M. blackburni + M. quinquemaculatus are sister taxa, and the monophyly of each species is supported with relatively high branch support under parsimony, maximum likelihood, and Bayesian inference. Manduca blackburni and M. quinquemaculatus also differ in genetic distance for CAD and COI, and we therefore consider them separate species. Thus, our molecular results corroborate previous studies on the morphology of M. blackburni and retain the species rank of this taxon. Our results also indicate that one or more South American subspecies of M. sexta may merit elevation to species.