Phylogenetic relationships among the subgenera Anopheles and Cellia were inferred from the D2 (36 species) and D3 (57 species) fragments of the 28S ribosomal DNA. Phylogenetic trees were reconstructed using parsimony, maximum likelihood and Bayesian methods. The resultant molecular phylogeny matched the classical morphological taxonomy reasonably well, and also resolved some ambiguities in the morphological taxonomy. Although a molecular phylogeny based on the D2 region did not change the traditional morphological character-based arrangement of anopheline taxa, some differences from the traditional arrangement were apparent in a phylogeny based on D3 fragment variation. This could, however, be due to the shorter length of the D3 fragment used in this study. Both the D2 and D3 data support the view that the subgenus Anopheles and the Neomyzomyia series are basal to the subgenus Cellia. The D2 data suggest a sister-group composed of Neocellia (Myzomyia Pyretophorus). The topology of the tree based on D2 variation supports the monophyly of all four series of the subgenus Cellia. In addition, the tree based on D3 variation suggests that the Neomyzomyia series is monophyletic, but additional species are required to support both these hypotheses. This kind of molecular approach, in combination with the existing morphological taxonomy, could help to resolve phylogenetic relationships among the anopheline mosquitoes.