The zebrafish mutation mother superior (mos m188 ) leads to a depletion of neural crest (NC) derivatives including the craniofacial cartilage skeleton, the peripheral nervous system (sympathetic neurons, dorsal root ganglia, enteric neurons), and pigment cells. The loss of derivatives is preceded by a reduction in NC-expressed transcription factors, snail1b, sox9b, sox10, and a specific loss of foxd3 expression in NC progenitor cells. We employed genetic linkage analysis and physical mapping to place the mos m188 mutation on zebrafish chromosome 6 in the vicinity of the foxd3 gene. Furthermore, we found that mos m188 does not complement the sym1/foxd3 mutation, indicating that mos m188 resides within the foxd3 locus. Injection of PAC clones containing the foxd3 gene into mos m188 embryos restored foxd3 expression in NC progenitors and suppressed the mos m188 phenotype. However, sequencing the foxd3 transcribed area in mos m188 embryos did not reveal nucleotide changes segregating with the mos m188 phenotype, implying that the mutation most likely resides outside the foxd3-coding region. Based on these findings, we propose that the mos m188 mutation perturbs a NC-specific foxd3 regulatory element. Further analysis of mos m188 mutants and foxd3 morphants revealed that NC cells are initially formed, suggesting that foxd3 function is required to maintain the pool of NC progenitors. Developmental Dynamics 235:3199 -3212, 2006.