Drosophila melanogaster FMRFamide-related peptides (FaRPs) include SDNFMRFamide, PDNFMRFamide, and TDVDHVFLRFamide (dromyosuppressin, DMS); each peptide contains a C-terminal FMRFamide but a different N-terminal extension. FaRPs and serotonin (5-HT) each affect the frequency of D. melanogaster heart contractions in vivo. We examined the cellular expression of FaRPs and 5-HT, and the activities of FMRFamide, SDNFMRFamide, PDNFMRFamide, or DMS and 5-HT on heart rate. FaRPs and 5-HT were not co-localized; FaRP-and 5-HT-immunoreactive fibers extended from different brain cells and innervated the anterior D. melanogaster dorsal vessel. However, no neuron expressed both a FaRP and 5-HT. The effect of FMRFamide and 5-HT was not different from the effect of 5-HT alone on heart rate. The effect of PDNFMRFamide and 5-HT showed an additive effect on heart rate. SDNFMRFamide and 5-HT or DMS and 5-HT resulted in non-additive effects on heart rate. Our data provide evidence for the complexity of FaRP and 5-HT interactions to regulate frequency of heart contractions in vivo. Our results also confirm the biological importance of FaRP N-terminal amino acid extensions.