SummaryMutations in theDMDgene lead to Duchenne muscular dystrophy, a severe X-linked neuromuscular disorder which manifests itself as young boys acquire motor functions. DMD is diagnosed after 2 to 4 years, but the absence of dystrophin has an impact before symptoms appear in patients, which poses a serious challenge in the optimization of standards of care. In this report, we investigated the early consequences of dystrophin deficiency during skeletal muscle development. We used single-cell transcriptome profiling to characterize the myogenic trajectory of human pluripotent stem cells and showed that DMD cells bifurcate to an alternative branch when they reach the somite stage. Here, dystrophin deficiency was linked to marked dysregulations of cell junction families involved in the cell state transitions characteristic of somitogenesis. Altogether, this work demonstrates thatin vitro, dystrophin deficiency has early consequences during myogenic development, which should be considered in future therapeutic strategies for DMD.