Motoneurons directly influence the differentiation of muscle fibers, regulating features such as muscle fiber type and receptor development. Less well understood is whether motoneurons direct earlier events, such as the patterning of the musculature. In Drosophila, the denervation of indirect flight muscles results in a diminished myoblast population and smaller or missing muscle fibers. We have examined whether the neuron-dependent control of myoblast number is due to regulation of cell division, motoneuron-dependent apoptosis, or nerve-dependent localization and migration of myoblasts. We found that denervation resulted in a reduced rate of cell division, as revealed by BrDU incorporation. There was no change in the frequency of apoptotic myoblasts following denervation. Using time lapse imaging of GFP-expressing myoblasts in vivo in pupae, we observed that despite denervation, the migration and localization of myoblasts remained unchanged. In addition to reducing myoblast proliferation, denervation also altered the segregation of myoblasts into the de novo arising dorso-ventral muscles (DVMs). To address this effect on muscle patterning, we examined the expression of the founder-cell marker Dumbfounded/Kirre (Duf) in imaginal pioneer cells. We show that there is a strong correspondence between cells that express Dumbfounded/Kirre and the number of DVM fibers, consistent with a role for these cells in establishing adult muscles. In the absence of innervation the Duf-positive cells are no longer detected, and muscle patterning is severely disrupted. Our results support a model where specialized founder cells prefigure the adult muscle fibers under the control of the nervous system.