Lutzomyia trapidoi is the major vector of cutaneous leishmaniasis in Ecuador. In the framework of an epidemiologic study, female Lu. trapidoi sand flies were captured on human bait in La Tablada and Paraiso Escondido. Some coloration heterogeneity among the specimens caught led us to look for the existence of cryptic species using multilocus enzyme electrophoresis. In 196 specimens studied, five of seven enzyme loci proved to be variable, making it possible to check for departures from panmixia both by Hardy-Weinberg statistics and linkage disequilibrium analysis. Two discrete groups were clearly distinguished, which could be differentiated by the diagnostic locus glycerophosphate dehydrogenase. The two groups occurred in sympatry within each locality. Genetic distances measured between these two groups were consistent with values usually found between distinct species. These results suggest the existence of at least two sibling species in Paraiso Escondido as well as La Tablada. The epidemiologic relevance of these results is discussed.