In zebrafish, the segmental series of pharyngeal arches is formed predominantly by two migratory cell types, neural crest and paraxial mesoderm, which arise in the early embryo. Neural crest cells migrate ventrally out of the neuroepithelium and into the arches to form cartilage, neurons, glia and pigment cells. Surrounding mesoderm generates muscles and endothelia. We labeled individual pharyngeal precursor cells with fluorescent dyes and found that their clonal progeny were confined to single segments and generated single cell types. When a neural crest or mesodermal cell was marked before migration into the pharynx, its progeny dispersed but generally remained confined to a single arch primordium. Such segmental restrictions arose first in the most rostral arches, mandibular and hyoid, and progressed caudally. The phenotypes of progeny generated by single cells were examined in the mandibular arch. Clones derived from premigratory neural crest cells generally did not contribute to more than one cell type. Further, the progenitors of some cell types were spatially separated in the premigratory crest. In particular, neurogenic crest cells were situated further laterally than cells that generate cartilage and connective tissues, while pigment and glial cell progenitors were more evenly distributed. Based on these results we suggest that arch precursors may be specified as to their eventual fates before the major morphogenetic movements that form the arch primordia. Further, cell movements are restricted during segmentation establishing a group of arch precursors as a unit of developmental patterning, as in the fashion of vertebrate rhombomeres or segmental lineage compartments in Drosophila.