Sox9 is a transcription factor related to campomelic dysplasia and sex reversal in human patients. Earlier studies in zebrafish led to the identification of two homologues of mammalian sox9, sox9a and sox9b. The present study represents the first evaluation of expression patterns of zebrafish sox9b during early embryogenesis. Our analyses reveal that sox9b transcripts are present throughout the life-cycle of the zebrafish, but exhibit tissue-specific distribution during embryogenesis. Zygotic expression of sox9b occurs in the anterolateral margins and the midline of the prospective dorsal neuroectoderm during late gastrulation. During early segmentation, the transcript is expressed in pairs of longitudinal bands in the prospective midbrain, hindbrain, and trunk, which identify the cranial and trunk neural crest progenitors. Neural crest cells cease expression of sox9b during migration, but some of their derivatives resume sox9b expression. Sox9b can serve as a marker for neural crest precursors.