Upon mating, females of many animal species undergo dramatic changes in their behavior. In Drosophila melanogaster, post-mating behaviors are triggered by sex peptide (SP), a key modulatory substance produced in the male seminal fluid and transferred to female during copulation. SP modulates female behaviors by acting on the sex peptide receptor (SPR) located in a small subset of internal sensory neurons that innervate the female uterus and project to the central nervous system (CNS). Interestingly, however, SPR is also expressed broadly in the CNS of both sexes. Moreover, SPR is also encoded in the genomes of insects that lack obvious SP orthologs. Based on these observations, we speculated that SPR may have additional ligands that are only distantly related to SP, if at all. If so, then this also raises questions on the evolution of SP-SPR signaling. To begin to address these questions, we set out to identify additional ligands for SPR. Here, we identify myoinhibitory peptides (MIPs) as a second family of SPR ligands that is conserved across a wide range of invertebrate species. MIPs are potent agonists for Drosophila, Aedes and Aplysia SPRs in vitro, yet are unable to trigger post-mating responses in vivo. In contrast to SP, MIPs are not produced in male reproductive organs, and are not required for post-mating behaviors in Drosophila females. We conclude that MIPs are evolutionarily conserved ligands for SPR, which are likely to mediate functions other than the regulation of female reproductive behaviors. Therefore, we propose that SPR has a different ancestral function, with a role in post-mating behavior arising only recently in Drosophila evolution, concomitant with the emergence of its novel SP ligand.