Ultradian rhythmic firing activity (period of 40–90 min) of a population of neurosecretory cells (NSCs) producing FXPRLamide peptides in the subesophageal ganglion (SG) of the silkmoth, Bombyx mori, is closely coordinated with periodically occurring electrical activity of developing flight muscles (FMs) during metamorphosis. To examine neuronal mechanisms and pathways that mediate the coordination of the NSC and flight motor systems, the ventral nerve cord (VNC) or circum-esophageal connectives were transected. Transection of the VNC between the SG and thoracic ganglia greatly shortened the period of activity rhythm of the FMs (5–15 min) with no effect on the rhythmicity of NSCs. Bilateral transsection of the circumesophageal connectives between the brain and SG abolished the rhythmic activity of NSCs, thereby suggesting that the coordination of the two systems may be mediated by a common oscillatory mechanism in the brain. Further, bisection of the brain in the midline failed to abolish the ultradian rhythmicity of FMs. Thus, each brain hemisphere may have an ultradian oscillator that activates the NSC system in the SG, and modulates the short-period oscillation of the flight motor system located in the thoracic ganglia.