Vitamin D, an essential regulator of calcium and phosphate homeostasis, is necessary for skeletal development. The active hormonal form of vitamin D functions through the vitamin D receptor (VDR), a member of the nuclear receptor family of transcription factors. The vdr mRNA and VDR protein are present in several cartilages of the skull in zebrafish embryos. To investigate the role of VDR on craniofacial cartilage development, vdr depletion experiments were performed. In zebrafish embryos, two distinct VDR genes (vdra and vdrb) have been identified. Knockdown of vdra has little effect on cartilage elements, whereas disrupting vdrb gene causes reduction and malformation of head cartilages. Remarkably, depletion of both vdra and vdrb produces more severe defects including complete loss of cartilage. These results strongly indicate that VDR signaling is essential for cartilage development in zebrafish. Previous studies in zebrafish revealed correct BMP signaling is required for cartilage formation in the skull. Interestingly, we show that knockdown of VDRs lead to increased expression of fsta, a BMP antagonist, in pharyngeal region around 36 hours post-fertilization. Taken together, these findings suggest that VDR may control cranial cartilage development by modulating BMP signaling.