Epidermal growth factor-like domain multiple 6 (Egfl6) is a basement membrane protein and plays an important role in hair follicle morphogenesis, angiogenesis, notochord development in vertebrates. Although expression in the developing head was observed in zebrafish, its role for craniofacial development and the determination of the pharyngeal region expressing , have not been reported yet. Here, we report the expression patterns and function of in craniofacial development in zebrafish. was expressed sequentially in the developing pharyngeal pouches that are key epithelial structures governing the development of the vertebrate head. However, loss-of-function mutations in did not cause any craniofacial defects, including the pouches as well as the thymus and facial cartilages whose development is contingent upon appropriate pouch formation. was unlikely redundant with expressed in a distinct pharyngeal region from that of in craniofacial development because reduction of with a MO in mutants did not affect craniofacial development. In addition, we found that carried an endogenous start loss mutation in the wild-type Tübingen strain, implying would be a non-functional gene. Taken all together, we suggest that expression in the pharyngeal pouches is not required for craniofacial development in zebrafish.