Myosin is a highly conserved, ubiquitous actin-based molecular motor that is distributed as diverse as from prokaryotes to mammalian tissues. Among various types in the myosin family proteins, class II, also called sarcomeric, myosin is a classical, conventional molecule that has been extensively studies on its functional and structural properties. It consists of two heavy chains (MYH) of about 200 kDa and four light chains of about 20 kDa. The exon-intron organization was determined for the major subunit of MYH, which contains ATP-hydrolysis and actin-binding sites, from torafugu (tiger pufferfish) Takifugu rubripes fast skeletal muscles. Comprehensive investigation for fast skeletal MYHs based on the fugu (torafugu) genome database and subsequent construction of their physical map revealed that torafugu contains at least 8 putative skeletal MYHs. Furthermore, genomic structural analysis revealed that skeletal MYHs are not clustered in a single locus, but rather spread to at least four loci, with two of them locating at the mammalian syntenic regions. Such arrangement of torafugu MYHs are in a marked contrast to mammalian fast skeletal MYHs that are clustered in a single locus. These data suggest that an ancient segmental duplication or whole-genome duplication occurred in fish lineage as in many other reported torafugu genes.