The phylogenetic relationships of Anopheles spp. at the junction of Oriental, Palearctic, and Afrotropical regions in the Iranian plateau were investigated using molecular markers. A 711-bp mitochondrial DNA cytochrome oxidase C subunit I (COI) fragment and the entire second internal transcribed spacer (ITS2) region (286–576 bp) of the nuclear ribosomal DNA (rDNA-ITS2) were sequenced from 14 and 28 taxa, respectively. The analyses included 12 species within Anopheles and 4 within the Myzorhynchus Series of the subgenus Anopheles, 8 within Neocellia, 6 within Myzomyia, 3 within Paramyzomyia, and 1 within the Pyretophorus Series of the subgenus Cellia. The congruent tree topologies of both molecular markers strongly supported monophyly of subgenera Anopheles and Cellia. Phylogenetic trees constructed on the basis of ITS2 sequences could accurately categorize all of the series according to the classical taxonomy but could not distinguish Pyretophorus (Anopheles subpictus) from Paramyzomyia Series. Although sequence data of the COI region were available for only 14 species, the inferred trees revealed good classification among the series but could not show the monophyletic relationship of Cellia spp. Except for a few cases, the tree inferred from ITS2 sequences revealed the best classification for the species studied. The molecular data could significantly improve our understanding of the phylogenetic position of the taxa.