A phylogenetic study, based on maximum parsimony, of ten species in the Anopheles punctulatus group of malaria vectors from the south-west Pacific was performed using structural and similarity-based DNA sequence alignments of the nuclear small ribosomal subunit (SSU = 18S). The structural alignment proved to be more informative than a computer generated similarity-based alignment. Analyses involving the full structural sequence alignment (2169 bp) and the helical regions (1547 bp) resolved a single tree of the same topology, while analyses using the similarity based alignment could not resolve the group. Studies on the three structural domains of the nuclear rDNA SSU identified domain 2 (769 bp) as the only region informative at the sibling-species level and resulted in the same tree as the full structural sequence and helical regions. The main conclusions of these studies were that the An. punctulatus group formed two clades: a Farauti clade containing members displaying an all black scaled proboscis (An. farauti 1–3 and 5–7) and a Punctulatus clade containing members that display some degree of white scaling on the proboscis (An. farauti 4, An. punctulatus and An. species near punctulatus). Anopheles koliensis can display either proboscis morphology and was positioned basal to the Farauti Clade. These results do not fully concord with those derived from the mitochondrial COII gene.