A new phylogenetic analysis of the Nyssorhynchus subgenus (Danoff-Burg and Conn, unpub. data) using six data sets {morphological (all life stages); scanning electron micrographs of eggs; nuclear ITS2 sequences; mitochondrial COII, ND2 and ND6 sequences} revealed different topologies when each data set was analyzed separately but no heterogeneity between the data sets using the arn test. Consequently, the most accurate estimate of the phylogeny was obtained when all the data were combined. This new phylogeny supports a monophyletic Nyssorhynchus subgenus but both previously recognized sections in the subgenus (Albimanus and Argyritarsis) were demonstrated to be paraphyletic relative to each other and four of the seven clades included species previously placed in both sections. One of these clades includes both Anopheles darlingi and An. albimanus, suggesting that the ability to vector malaria effectively may have originated once in this subgenus. Both a conserved (315 bp) and a variable (425 bp) region of the mitochondrial COI gene from 15 populations of An. darlingi from Belize, Bolivia, Brazil, French Guiana, Peru and Venezuela were used to examine the evolutionary history of this species and to test several analytical assumptions. Results demonstrated (1) parsimony analysis is equally informative compared to distance analysis using NJ; (2) clades or clusters are more strongly supported when these two regions are combined compared to either region separately; (3) evidence (in the form of remnants of older haplotype lineages) for two colonization events; and (4) significant genetic divergence within the population from Peixoto de Azevedo (State of Mato Grosso, Brazil). The oldest lineage includes populations from Peixoto, Boa Vista (State of Roraima) and Dourado (State of São Paulo).