Drosophila melanogaster pupae are exposed to many biotic and abiotic dangers while immobilized during several days of metamorphosis. As a passive defense mechanism, appropriate pupation site selection represents an important mitigation of these threats. Pupation site selection is sensitive to genetic and environmental influences, but the specific mechanisms of the behavior are largely unknown. Using a set of 76 recombinant inbred strains we identify a single quantitative trait locus, at polytene position 56A01-C11, associated with pupation site variation. We furthermore present a detailed investigation into the wandering behaviors of two strains expressing different pupation position tendencies, and identify behavioral differences. Larvae from a strain that tends to pupate relatively far from the food also tend to travel significantly farther from the media during wandering. We did not observe consistent differences in either the number or duration of wandering forays made by near or far pupating strains. The ability of larvae to integrate several internal and external environmental cues while choosing a contextually appropriate pupation site, and specifically, the variation in this ability, presents a very interesting behavioral phenotype in this highly tractable genetic model organism.