To understand the genetics and evolution of foraging in larvae of Drosophila funebris, we examined two strains reared at different breeding sites in the wild. Larvae of the Til-Til strain breed in necrotic cactus tissue, while those of the Pelequén strain rear in necrotic prickly pear cladodes. We measured feeding, locomotion, turning behavior, and latency of D. funebris. Til-Til and Pelequén larvae, at 8 days of age show very similar rates in all behaviors. Crosses between Til-Til and Pelequén strains decrease feeding rate and increase locomotion, turning, and latency in F(1) and F(2) larvae. Backcross larvae show a behavior similar to that of their parental strains. The behavioral similarities observed between the Til-Til and Pelequén strains are product of two different co-adapted gene pools. Epistasis and dominance are the principal sources upon which adaptation of the gene pools of each population are based.