Retinoic acid (RA) plays essential roles in vertebrate embryogenesis. However, vertebrates cannot synthesize RA de novo. They synthesize it by two oxidative steps, first converting the precursor vitamin A into retinal by retinol dehydrogenase, and then oxidizing retinal into RA irreversibly by retinal dehydrogenase. It is known that vitamin A deficiency (VAD) causes Vitamin A Deficiency Syndrome in animals including quail, mouse, rat, and human. However, little is known about the effects of VAD on zebrafish embryogenesis. In this study, we obtained zebrafish VAD embryos from the zebrafish fed a retinoids-free diet. By analyzing the VAD embryos, we found that VAD caused asymmetric somitogenesis and abnormal hindbrain patterning in zebrafish embryos. However, the phenotype of defected hindbrain in VAD embryos was not as severe as that in the embryos in which aldh1a2, the major gene that is responsible for RA synthesis in zebrafish early development, was knocked down, or the embryos treated with 10 mmol/L DEAB (diethylaminobenzaldehyde, inhibitor of retinal dehydrogenases). Our results indicated that the VAD embryos were short of but not free of vitamin A, and they might also have a RA generation pathway independent of retinal dehydrogenase.