Anopheles halophylus Silva-do-Nascimento & Lourenço-de-Oliveira was recently described using morphological and biological variants in specimens previously identified as Anopheles triannulatus (Neiva & Pinto). Because these two species occur in sympatry in central Brazil, we used allozymes to determine the extent of gene flow to confirm that they are different species. Of 11 allozyme loci analyzed, one (Mpi) was found to be diagnostic for An. halophylus and An. triannulatus, confirming their specific status. This locus revealed a second sibling species within An. triannulatus sensu lato. An. halophylus and the new undescribed species were confirmed using random amplified polymorphic DNA markers that showed moderate genetic divergence among these three sympatric and closely related taxa (D = 0.145–0.428). Moreover, this marker indicates that An. halophylus and the new species are more closely related to each other than either is to An. triannulatus.