Lutzomyia longipalpis (Lutz & Neiva) is the primary vector of visceral leishmaniasis in Venezuela. An analysis of alleles at seven enzyme-encoding loci among four populations from different geographic and epidemiological regions revealed strong genetic substructuring. Isozyme analysis indicated that L. longipalpis in Venezuela is a complex of at least two subspecies. Possible differences in population size during their evolutionary histories, varying colonization histories and geological events may explain discrepancies in the patterns of variation observed at genetic markers between these four populations.