The post-mating response induced by male-derived sex-peptide in Drosophila females is a wellestablished model to elucidate how complex innate behaviors are hard-wired into the brain. Here, we found that the channel nuclear pore protein Nup54 is essential for the sex-peptide response as viable mutant alleles do not lay eggs and reduce receptivity upon sex-peptide exposure. Nup54 directs correct wiring of few adult brain neurons that express pickpocket and are required for egg laying, but channel Nups also mediate sexual differentiation and male X-chromosome dosage compensation. Consistent with links of Nups to speciation, the Nup54 promoter is a hot spot for rapid evolution and Nup54 is differentially expressed in the brain. These results implicate altered expression of Nup54 to the onset of speciation processes leading to changes in neuronal wiring and sexual differentiation as a response to sexual conflict arising from male-derived SP to direct the female post-mating response.