Lutzomyia longipalpis, a sibling complex, is the main vector of Leishmania chagasi/infantum. Discriminating between siblings is important as they may differ in vectorial capacity. Lutzomyia longipalpis populations display distinct male sex pheromone chemotypes. We investigated the phylogeographic pattern of variation at microsatellite loci from 11 populations from Brazil and Venezuela related to their male pheromone. Temporal genetic differentiation was mostly not significant at the same site. Spatial genetic differentiation was, however, strong, although there was only a weak relationship between genetic differentiation and the geographic distance separating the samples (r ² < 0.10); geographic separation explained a much greater (54-97%) percentage of the genetic differences among populations when samples with the same pheromone type were analyzed separately. A cluster analysis showed five groups: Lu. cruzi (Brazil) and Lu. pseudolongipalpis (Venezuela) as separate species, two (mostly 9-methyl-germacrene-B) Venezuelan and Brazilian groups, and a very distinct cluster of Brazilian cembrene populations.