The Yes-associated protein (YAP) is a small protein that binds to many transcription factors and modulates their activity. Bioinformatics analysis indicated that zebrafish Yap shares high identity with its orthologs in fruit fly, chicken, mouse, and human. Expression analysis revealed that maternal transcripts of yap are ubiquitous, and endogenous yap is chronologically expressed in the notochord, brain, eyes, branchial arches, and pectoral fins. Knockdown of yap causes distinct morphological defects in embryos, which display a small head with smaller eyes than normal and fewer cartilages in the branchial arches. Proneural and neuronal gene expression in yap morphant brain is significantly reduced. The expression of crestin is also markedly reduced in all recognizable arch-associated regions of yap morphants. Furthermore, TUNEL analysis revealed that there is a marked increase in cell death in yap morphant brain. In conclusion, zebrafish yap is required for the development of the brain, eyes, and neural crest during embryogenesis.