The myotome is a segmented paraxial muscle present in all early vertebrate embryos, which in amniotes disappears in mid-embryogenesis, and is replaced by complex epaxial and hypaxial musculature. Little is known about how this transition occurs. Here, we describe the detailed morphogenesis of the epaxial muscles from the epaxial myotome, in rodent embryos. The results show there is no apoptosis of myotomal fibres during the transition, and that the epaxial muscles arise by translocation, re-orientation, and elongation of the myotomal myocytes followed by cleavage of the myotomal masses. Myotomal myocytes transit from a mononucleated to a multinucleated state just before onset of this transformation. Each newly-formed epaxial muscle anlagen includes populations of Pax3- and Pax7-positive muscle progenitors, with different distributions. Using transgenic mouse embryos bearing a GFP marker for Scleraxis, we show that tendon progenitors are tightly associated with the sides and ends of myotomal myocytes as they re-orient and elongate. Developmental Dynamics 239:2898–2910, 2010. © 2010 Wiley-Liss, Inc.