Lingering questions regarding the current classification of the Neotropical subgenera Kerteszia and Nyssorhynchus of the genus Anopheles are addressed on the basis of comparative morphological data. Homologous characters in the adult, male genitalia, pupa and larva are compared and discussed. The validity of the two subgenera is affirmed using synapomorphic characters. Some interesting characteristics of the immature stages are also considered in terms of ontogeny and heterochrony. The Myzorhynchella Section of the subgenus Nyssorhynchus is characterized and contrasted with the Albimanus and Argyritarsis sections for the first time. A brief overview of the history and current status of classification of the genus Anopheles and the subgenera Kerteszia and Nyssorhynchus is presented.