Many neuropeptides have been widely conserved across species during evolution. Valuable insights may be gained by studying their biological activity in different species and identifying common functions. Standard basic local alignment search tool for proteins (BLASTP) searches often fail to detect homologous counterparts in distantly related species such as Drosophila and Caenorhabditis elegans, despite evidence for functional equivalents. This can be remedied by employing distant homology BLASTP with less stringent search parameters. Here, I describe the use of BLASTP searches with relaxed settings to identify the functional counterparts of kisspeptin and amylin or islet amyloid polypeptide (IAPP) in C. elegans. By increasing the E-value and relaxing other parameters, the list of potential homologs was expanded. Follow-up analysis to validate attractive hits included searches with sequences of neuropeptides from other species and convergence of the search results on recurring hits. Strong candidates for functional counterparts of kisspeptin and IAPP were found with this approach. Moreover, the hybrid structure (part RFamide and part calcitonin-like hormone) of one hit—FLP-12—suggested that a shared distant ancestor may have been duplicated and the two copies then diverged into separate RFamide and peptide hormone families. Low homology BLASTP searching is a powerful method for identifying distant relatives of neuropeptides and for characterizing their evolutionary relationship to ancient common ancestors.