The Anopheles punctulatus (Diptera: Culicidae) group is the main vector for malaria and Bancroftian filariasis in Vanuatu. Anopheles larvae were collected from 10 localities on five islands of Vanuatu during the 2004 dry season for species identification as well as for estimating population structure and gene flow within and among islands. Species identification was determined using polymerase chain reaction-restriction fragment length polymorphism analysis of the internal transcribed spacer 2 region. Population structure and gene flow were examined by sequencing a portion of the ND4/ND5 region of the mitochondrial genome. Only one species of the An. punctulatus group, An. farauti s.s., was identified, consistent with previous studies in Vanuatu. A nonrandom distribution of An. farauti s.s. lineages was observed with one cosmopolitan lineage shared by eight sites on all five islands and a preponderance of island-specific lineages (36/40), indicating the introduction of a single main lineage into Vanuatu followed by dispersal, diversification, and limited lineage exchange between islands. Network analysis suggests a possible second introduction of An. farauti s.s. into the northern islands of Gaua and Malekula. Gene flow was high on three of the five islands, whereas Tanna and Santo have significant population structure. Among islands, gene flow was limited, indicating active mosquito dispersal only over short distances and a paucity of passive human-mediated dispersal over long distances. Minimal risk of active dispersal among these islands indicates that vector control can be effectively initiated at the island level within the archipelago of Vanuatu.