We used two mitochondrial loci (nicotinamide adenine dinucleotide dehydrogenase subunit 4 and cytochrome oxidase II) and a nuclear locus (28S-D2 spacer) for a total of 1337 bp to evaluate the relationships among the four subspecies of Aedes (Finlaya) japonicus Theobald. Ae. j. japonicus was recently introduced into the United States and has been expanding rapidly. We also included in our analysis a morphologically very closely related species, Aedes (Finlaya) koreicus Edwards, as well as three more distantly related species: Aedes (Finlaya) togoi Theobald, Aedes (Finlaya) hatorii Yamada, and Aedes (Aedimorphus) vexans Meigen. We found that the four subspecies in the Ae. japonicus complex are genetically quite distinct but seem to form a monophyletic group that surprisingly also includes Ae. koreicus, suggesting the need for a taxonomic reconsideration of the group. We also found that the two southern subspecies are more closely related to each other than to any of the remaining subspecies or to Ae. koreicus and may indicate an ancient north—south split of the lineage. Considering the overlap between Ae. j. japonicus and Ae. koreicus, but the stronger association between Ae. koreicus and humans, we are surprised it also has not expanded from its original range. As a proactive reaction to this possibility, we designed and tested a DNA-based rapid assay to differentiate Ae. koreicus from some of the species with which it may be confused in the United States. These Aedes are putative vectors of several important viral encephalitides.