We used zebrafish as a model to study the biological functions of NF-YB during early development. Both RT-PCR and whole-mount in situ hybridization experiments revealed that nf-yb was a maternally inherited gene. Later, its expression was restricted in the future head cartilages as well as in the developing notochord. Embryos after injection with nf-yb-morpholino displayed reduced-head phenotypes, including smaller head (WT, length of head, L: 0.515 ± 0.019 mm, width of head, W: 0.323 ± 0.077 mm; nf-yb-morphant, L: 0.347 ± 0.037 mm; W: 0.266 ± 0.018 mm), sharpen Meckel's cartilage, loss of ceratobranchial, and enlarged angles of ceratohyal (WT: 72.6 ± 9.4°; nf-yb-morphant: 110.0 ± 32.5°). Subsequently, those abnormalities can be rescued after injection with capped nf-yb mRNA. TUNEL assay suggested that large amounts of cell apoptosis appeared in the head region of nf-yb-morphants. Staining with digoxigenin-labeled dlx2a, sox9a, runx2b and col2a1 riboprobes showed that nf-yb-morphants displayed reduced amounts of cranial neural crest cells which are required for mandibular and branchial arches formation. These observations clearly indicate that knockdown of nf-yb translation induced parts of cranial neural crest cells apoptosis, affected cartilages formation and consequently caused reduced-head phenotypes. These findings uncover a novel and unexpected role for NF-YB as a critical modulator of neural crest cell's gene expression governing embryonic cartilage growth.