Faithful innervation of the diaphragm is essential for normal muscular function, but our understanding of this process is less clear than it is for other muscular systems. Here (p. 3295), Maximilian Saller, Andrea Huber and colleagues investigate targeting and innervation of the diaphragm by phrenic nerves. The authors use a genetic approach to study the involvement of the Sema3–Npn-1 signalling pathway in phrenic nerve targeting and fasciculated growth during establishment of the diaphragm in mice. The authors show that systemic ablation of Npn-1 does not impact the initial branch formation and guidance of the phrenic nerves. However, Sema3–Npn-1 signalling does govern phrenic nerve fasciculation and branching during innervation of the costal muscles of the diaphragm in a cell autonomous manner. Interestingly, phrenic axons misproject into the central tendon region of the diaphragm and innervate ectopic muscles in the absence of Sema3–Npn-1 signalling, leading the authors to hypothesise that additional factors released by misprojecting growth cones cause ectopic myocyte fusion. Next, the authors demonstrate that Slit2 and Robo1, members of an axon-guidance-cue family, are expressed in phrenic motor neurons and migrating myoblasts, respectively, during diaphragm innervation. Further, Slit1 and Slit2 exert an attractive effect on primary myoblasts. This paper provides important new insights into both phrenic nerve development and myocyte fusion.