In the subgenus Nyssorhynchus of the Neotropical Anophelines, An. nuneztovari is a well-known malaria vector in portions of Colombia and Venezuela, but evidently not east of the Orinoco or in the Amazon basin. Populations previously found to differ in behavioral ecology and by a fixed chromosome inversion were examined for up to 23 electrophoretically detectable allozyme loci. We found genetic heterozygosity to be on a par with other insects studied by this method. However, we found that genetic identities estimated from the allozyme data suggest a lack of genic identities indicating that divergence may be a relatively recent event in the evolutionary history of the chromosomally distinct populations.