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Applying degenerate polymerase chain reaction using primers specific for the conserved forkhead domain, we identified zebrafish <jats:italic>foxe1<\/jats:italic> (<jats:italic>foxe1<\/jats:italic>). Foxe1 is expressed in the thyroid, pharynx, and pharyngeal skeleton during development; strongly expressed in the gill and weakly expressed in the brain, eye, and heart in adult zebrafish. A loss of function of foxe1 by morpholino antisense oligo (MO) exhibited abnormal craniofacial development, shortening of Meckel's cartilage and the ceratohyals, and suppressed chondrycytic proliferation. However, at 27\u2009hr post fertilization, the <jats:italic>foxe1<\/jats:italic> MO\u2010injected embryos showed normal <jats:italic>dlx2<\/jats:italic>, <jats:italic>hoxa2<\/jats:italic>, and <jats:italic>hoxb2<\/jats:italic> expression, suggesting that the initial steps of pharyngeal skeletal development, including neural crest migration and specification of the pharyngeal arch occurred normally. In contrast, at 2 dpf, a severe reduction in the expression of <jats:italic>sox9a<\/jats:italic>, <jats:italic>colIIaI<\/jats:italic>, and <jats:italic>runx2b<\/jats:italic>, which play roles in chondrocytic proliferation and differentiation, was observed. Interestingly, <jats:italic>fgfr2<\/jats:italic> was strongly upregulated in the branchial arches of the <jats:italic>foxe1<\/jats:italic> MO\u2010injected embryos. Unlike <jats:italic>Foxe1<\/jats:italic>\u2010null mice, normal thyroid development in terms of morphology and thyroid\u2010specific marker expression was observed in <jats:italic>foxe1<\/jats:italic> MO\u2010injected zebrafish embryos. Taken together, our results indicate that Foxe1 plays an important role in chondrogenesis during development of the pharyngeal skeleton in zebrafish, probably through regulation of <jats:italic>fgfr2<\/jats:italic> expression. Furthermore, the roles reported for FOXE1 in mammalian thyroid development may have been acquired during evolution. <jats:italic>J. Exp. Zool. (Mol. Dev. 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