Two mosquito species of the subgenus Stegomyia (genus Aedes) (Diptera: Culicidae) on the islands of Palau and Yap (Aedes dybasi Bohart and Aedes maehleri Bohart) are adapted to aquatic habitats occupied by Nepenthes pitcher plants. To reveal the origin of these pitcher plant mosquitoes, we attempted a molecular phylogenetic analysis with 11 Stegomyia species by using sequence data from mitochondrial cytochrome oxidase subunit I and 16SrRNA genes as well as the nuclear 28SrRNA gene. Ae. dybasi, a pitcher plant specialist, was sister to Aedes palauensis Bohart within the scutellaris group from the same islands. Ae. maehleri, an opportunistic pitcher plant mosquito, was in a distinct lineage related to the scutellaris group. The adaptation to pitcher plants could have occurred independently in these two species, and recent differentiation of the pitcher plant mosquito Ae. dybasi from the nonpitcher plant mosquito Ae. palauensis was suggested by a relatively small sequence divergence between these species. We also discuss the implications of this analysis for the phylogeny of some other Stegomyia species.