The phlebotomine sand fly, Lutzomyia verrucarum, is one of the principle vectors of cutaneous leishmaniasis, however, its distribution and movement is poorly understood. Sand fly collections and disease case reports from January-March in 2006 indicate vector populations have increased their endemic ranges. The expanding geographic range emphasizes the importance of defining the abiotic factors that delimit sand fly habitat and migration. To identify sand fly migration barriers in Ancash, Peru, three neighboring valleys (costal, interandean, and interior) were selected based on distinct L. verrucarum populations and the geographic landscape characteristics between populations. Genetically similar populations were identified by collecting 15 L. verrucarum from each of three villages per valley. Sand fly population structure was determined by the amplification and direct sequencing portions of mitochondrial genes (1,400 bp NADH and 800 bp cytochorme b) and nuclear genes (an intron of 188 bp within the elongation factor 1α and a 300 bp intron within tubulin β). A gene network, based on base pair variation in the sequences, was then visualized with the computer program TCS. Lutzomyia verrucarum from the neighboring Lima provided an outgroup comparison. To define sand fly habitat, autologistic analysis correlated sand fly presence with 50-year averages of precipitation and minimum, maximum and mean temperatures from remotely sensed weather data. Environmental barriers were identified by comparing the number of migrants per generation, determined from the gene network, with the abiotic conditions surrounding the suitable sand fly habitats. The data indicate that elevation and temperature create genetic structuring within the valley systems.