Myogenic regulatory factors of the Myod family (MRFs) are transcription factors essential for mammalian skeletal myogenesis. However, the roles of each gene in myogenesis remain unclear, owing partly to genetic linkage at the Myf5/Mrf4 locus and to rapid morphogenetic movements in the amniote somite. In mice, Myf5 is essential for the earliest epaxial myogenesis, whereas Myod is required for timely differentiation of hypaxially derived muscle. A second major subdivision of the somite is between primaxial muscle of the somite proper and abaxial somite-derived migratory muscle precursors. Here, we use a combination of mutant and morphant analysis to ablate the function of each of the four conserved MRF genes in zebrafish, an organism that has retained a more ancestral bodyplan. We show that a fundamental distinction in somite myogenesis is into medial versus lateral compartments, which correspond to neither epaxial/hypaxial nor primaxial/abaxial subdivisions. In the medial compartment, Myf5 and/or Myod drive adaxial slow fibre and medial fast fibre differentiation. Myod-driven Myogenin activity alone is sufficient for lateral fast somitic and pectoral fin fibre formation from the lateral compartment, as well as for cranial myogenesis. Myogenin activity is a significant contributor to fast fibre differentiation. Mrf4 does not contribute to early myogenesis in zebrafish. We suggest that the differential use of duplicated MRF paralogues in this novel two-component myogenic system facilitated the diversification of vertebrates.KEY WORDS: Muscle, Zebrafish, Myosin, Slow, Fibre, Fast, Head, Fin, mrf4 (myf6), myod, myf5, Myogenin, Hedgehog, prdm1, pax3, meox1, hsp90, mef2d Development 136, 403-414 (2009) Here, we turn to zebrafish in the hope of finding shared and divergent roles for individual MRFs in myogenesis. Each zebrafish somite generates at least four populations of muscle fibres within the first 15 hours of somitogenesis, a timing and diversity that are akin to amniote somite myogenesis (Kahane et al., 2001;Kassar-Duchossoy et al., 2004). Two Hedgehog (Hh)-dependent medial mononucleate slow muscle fibre types derive from the myf5-and myod-expressing adaxial cells lying adjacent to the notochord (Blagden et al., 1997;Coutelle et al., 2001;Weinberg et al., 1996;Wolff et al., 2003). Approximately three muscle pioneer fibres remain at the dorsoventral midline, whereas 20 superficial slow fibres migrate to the lateral myotome surface (Devoto et al., 1996). More lateral paraxial cells within the somite also express the MRFs myf5 and myod (Coutelle et al., 2001;Weinberg et al., 1996) and give rise to two kinds of multinucleate fast fibre: the Fgf8-dependent lateral fast fibres and the Fgf8-independent medial fast fibres, a subset of which becomes the fast Engrailed-expressing cells as a result of later Hh signalling (Groves et al., 2005;Wolff et al., 2003). Both slow and fast lineage cells also express myog and mrf4 Weinberg et al., 1996). Using predicted null mutations in myf5 and mrf4 and morpholino antisense oligo...