The complete sequencing of the Drosophila melanogaster genome allowed major progress in the research on invertebrate neuropeptide signaling. However, it is still largely unknown how the insect CNS exerts synaptic control over the secretory activity of peptidergic neurons; afferent pathways and employed chemical transmitters remain largely unidentified. In the present study, we set out to identify neurotransmitters mediating synaptic input onto CCAP-expressing neurons (N(CCAP)), which play an important role in the regulation of ecdysis-related events. By in vitro and in situ calcium imaging with synthetic and genetically encoded calcium indicators, we provide evidence that differential neurotransmitter inputs control the activity of N(CCAP) subsets. In short-term culture, almost all N(CCAP) showed increases of the free intracellular calcium concentration after application of acetylcholine (ACh) and nicotine, whereas only some N(CCAP) responded to glutamate and GABA. In the intact ventral ganglia of both larvae and adults, only few N(CCAP) showed intracellular calcium-rises or calcium-oscillations after application of cholinergic agonists indicating a prevailing central inhibition of most N(CCAP) during these developmental stages. In larvae, responding N(CCAP) were primarily located in the third thoracic neuromere. At least one N(CCAP) pair in this neuromere belonged to a morphologically distinct subset with neurohemal endings on the body wall muscles. Our results suggest that N(CCAP) express functional receptors for ACh, glutamate, and GABA, and indicate that these transmitters are involved in a context-dependent regulation of functionally distinct N(CCAP) subsets.