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<p>Abstract</p> <p>Background</p> <p>The mosquito <it>Anopheles irenicus</it>, a member of the <it>Anopheles punctulatus </it>group, is geographically restricted to Guadalcanal in the Solomon Islands. It shows remarkable morphological similarities to one of its sibling species, <it>An. farauti sensu stricto </it>(<it>An. farauti s.s</it>.), but is dissimilar in host and habitat preferences. To infer the genetic variations between these two species, we have analyzed mitochondrial <it>cytochrome oxidase subunit II </it>(<it>COII</it>) and nuclear ribosomal <it>internal transcribed spacer 2 </it>(<it>ITS2</it>) sequences from Guadalcanal and from one of its nearest neighbours, Malaita, in the Solomon Islands.</p> <p>Results</p> <p><it>An. farauti s.s</it>. was collected mostly from brackish water and by the human bait method on both islands, whereas <it>An. irenicus </it>was only collected from fresh water bodies on Guadalcanal Island. <it>An. irenicus </it>is distributed evenly with <it>An. farauti s.s</it>. (Φ_SC= 0.033, 0.38%) and its range overlaps in three of the seven sampling sites. However, there is a significant population genetic structure between the species (Φ_CT= 0.863, <it>P </it>< 0.01; Φ_ST= 0.865, <it>P </it>< 0.01 and <it>F</it>_ST= 0.878, <it>P </it>< 0.01). Phylogenetic analyses suggest that <it>An. irenicus </it>is a monophyletic species, not a hybrid, and is closely related to the <it>An. farauti s.s</it>. on Guadalcanal. The time estimator suggests that <it>An. irenicus </it>diverged from the ancestral <it>An. farauti s.s</it>. on Guadalcanal within 29,000 years before present (BP). <it>An. farauti s.s</it>. expanded much earlier on Malaita (<it>t</it>_exp= 24,600 BP) than the populations on Guadalcanal (<it>t</it>_exp= 16,800 BP for <it>An. farauti s.s</it>. and 14,000 BP for <it>An. irenicus</it>).</p> <p>Conclusion</p> <p>These findings suggest that <it>An. irenicus </it>and <it>An. farauti s.s</it>. are monophyletic sister species living in sympatry, and their populations on Guadalcanal have recently expanded. Consequently, the findings further suggest that <it>An. irenicus </it>diverged from the ancestral <it>An. farauti s.s</it>. on Guadalcanal.</p>