Vertebrate skeletal muscles arise from two major types of precursor cell populations which differentiate into slow and fast fibers. Six1 homeodomain transcription factor was implicated in myogenesis in mammals, but its role in the development of different types of muscle precursors remained unclear. In zebrafish, there are two close homologs of Six1: six1a (known earlier as six1) and six1b identified in this study. Here we studied the role of six1a whose expression is initiated in the fast muscle precursor region of the forming somite. In the six1a loss-of-function conditions, initiation of myog expression was compromised in fast muscle precursors whereas myod expression appeared unaffected suggestive of six1a requirement for fast muscle differentiation. Expression of myog recovered soon, but differentiation of fast muscle proceeded abnormally. Exclusion of muscle-specific transcripts, myhz1 and tpma, from the dorsal and posterior part of somites demonstrated early abnormalities in fast muscle formation. U-shaped somites, reduced birefringence, and abnormal cell morphology were observed in morphant fast muscle upon terminal differentiation. In contrast, differentiation of slow fibers appeared largely unaffected. We conclude that Six1a plays an essential role at the onset of fast muscle differentiation.