We cloned three full-length cDNAs encoding myosin heavy chains (MYHs) previously found to be expressed in embryos or larvae of medaka Oryzias latipes. Based on cDNA sequence information, the three medaka MYH genes, mMYH emb1 , mMYH L1 and mMYH L2 , were localized on the chromosomes. In vivo promoter assay using the gene encoding green or red fluorescent protein and linked to the 5 0 -flanking region of mMYH demonstrated that the transcripts of fast-type mMYH emb1 , first expressed in embryos but belonging to the adult type in phylogenetic analysis, were located in the horizontal myoseptum. On the other hand, embryonic fast-type mMYH L1 and mMYH L2 were expressed in the whole myotomes. Interestingly, cells expressing mMYH emb1 were localized together with engrailed, and cyclopamine, which blocks hedgehog signaling, inhibited mMYH emb1 expression as well as the formation of the horizontal myoseptum, suggesting that muscle pioneer cells express mMYH emb1 as a key protein in the formation of the horizontal myoseptum.