Anopheles darlingi is the most important malaria vector in the Amazon basin of South America, and is capable of transmitting both Plasmodium falciparum and P. vivax. To understand the genetic structure of this vector in the Amazonian region of Peru, a simple polymerase chain reaction (PCR)-based test to identify this species of mosquito was used. A random amplified polymorphic DNA-PCR was used to study genetic variation at the micro-geographic level in nine geographically separate populations of An. darlingi collected in areas with different degrees of deforestation surrounding the city of Iquitos. Within-population genetic diversity in nine populations, as quantified by the expected heterozygosity (HE), ranged from 0.27 to 0.32. Average genetic distance (FST) among these populations was 0.017. These results show that the nine studied populations are highly homogeneous, suggesting that strategies can be developed to combat this malaria vector as a single epidemiologic unit.