A morphological comparison and molecular study of the Afrotropical Funestus and Afro-Oriental Minimus groups within the Myzomyia series of Anopheles (Cellia) was conducted to determine their phylogenetic affinities. Relationships were investigated using morphological characters and ribosomal (D3) and mitochondrial (COII) nucleotide sequences. Cross-identification of specimens from one group by using keys for the other group confirmed their morphological similarity, i.e., members of one group shared the key characters with members of the other group. Molecular analyses recognized five clades, not strictly related to geographical distribution: the Aconitus, Culicifacies, Funestus, Minimus, and Rivulorum subgroups. Morphological observations were congruent with the results of molecular analyses. Anopheles leesoni, an Afrotropical species, is closely related to the Oriental Minimus complex, and these taxa share a close relationship with the Fluviatilis complex that occurs from the Arabian Peninsula through India. The immature and adult stages of An. rivulorum in Africa bear morphological characters that distinguish this species from members of the Afrotropical Funestus subgroup. A composite scheme of classification based on the results and previously published information is proposed for the two groups. It is noted that An. fluviatilis species S is conspecific with An. minimus species C.