To evaluate whether environmental heterogeneity contributes to the genetic heterogeneity in
Anopheles triannulatus
, larval habitat characteristics across the Brazilian states of Roraima and Pará and genetic sequences were examined. A comparison with
Anopheles goeldii
was utilised to determine whether high genetic diversity was unique to
An. triannulatus. Student
t test and analysis of variance found no differences in habitat characteristics between the species. Analysis of population structure of
An. triannulatus and
An. goeldii revealed distinct demographic histories in a largely overlapping geographic range. Cytochrome oxidase I sequence parsimony networks found geographic clustering for both species; however nuclear marker networks depicted
An. triannulatus with a more complex history of fragmentation, secondary contact and recent divergence. Evidence of Pleistocene expansions suggests both species are more likely to be genetically structured by geographic and ecological barriers than demography. We hypothesise that niche partitioning is a driving force for diversity, particularly in
An. triannulatus.
