Morphological identification of the mealybug species Planococcus citri (Risso) and P. minor (Maskell), two serious agricultural pests, is often complicated by the existence of intermediate forms and a lack of knowledge of the intraspecific variation that occurs in each species. In this study, we have explored the utility of two molecular markers, the mitochondrial gene cytochrome oxidase I (COI) and the nuclear gene, elongation factor 1α (EF-1α) to ascertain the identity of these species and to provide reliable characters for their identification. Results from maximum parsimony analysis of DNA sequence data from both genes indicate the existence of a third clade from the Hawaiian Islands, whose members are distinct from both P. citri and P. minor. The individuals that group in this additional clade, although morphologically identical to P. citri, cluster with P. minor in ≈50% of the cladograms obtained with the COI, and 80% of the cladograms obtained with EF-1α. Our studies show that COI, in combination with morphological and geographical data, can be used to accurately identify the P. minor clade, the P. citri clade, and the clade from the Hawaiian Islands in most cases. Given a few instances in which identification resulting from COI and EF-1α were in conflict, however, our results must be interpreted with caution and until additional studies are performed, no changes are proposed in the taxonomy of this species complex.