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Lutzomyia longipalpis is the main vector of an important neglected disease in America. The genetic diversity of this vector was estimated in the population collected in two geographical areas separated by up to 37 km. We analyzed the sequence CB3-PDR / N1 N-PDR of 22 individuals obtaining a parameter of: h = 0.43 and tt = 0.0017 (Bona), h = 0.89, tt = 0.004 (The Lemon) with a genetic differentiation of kst = 0.03; p> 0.05 between them. Eight haplotypes were detected, of which it was shared. A significant differentiation was detected between the Panama-Colombia (kst = 0.98), Panama-Costa Rica (kst = 0.98) and Panama-Brazil (kst = 0.72) populations under the isolation model. The genetic inferences of this population can complement the dispersion information and provide important clues to understand the ecology of Lutzomyia longipalpis in Panama. [ABSTRACT FROM AUTHOR]