By acquiring wings, bats are the only mammalian lineage to have achieved flight. To be capable of powered flight, they have unique muscles associated with their wing. However, the developmental origins of bat wing muscles, and the underlying molecular and cellular mechanisms are unknown. Here we report, first, that the wing muscles are derived from multiple myogenic sources with different embryonic origins, and second, that there is a spatiotemporal correlation between the outgrowth of wing membranes and the expansion of wing muscles into them. Together, these findings imply that the wing membrane itself may regulate the patterning of wing muscles. Last, through comparative gene expression analysis, we show Fgf10 signalling is uniquely activated in the primordia of wing membranes. Our results demonstrate how components of Fgf signalling are likely to be involved in the development and evolution of novel complex adaptive traits.