Neural crest cells (NCC) are vertebrate-specific multipotent progenitor cells that arise from the neural plate border and go on to contribute to a wide variety of morphological structures such as the jaw and palate, enteric nervous system (ENS), and pigment cells. Defects in essential steps in neural crest cell development have been associated with a wide variety of congenital disorders, collectively referred to as neurocristopathies. Her9/Hes4 is a bHLH-O transcriptional repressor that has been shown to regulate neural crest cell and craniofacial development in Xenopus and zebrafish, however the extent of Her9 function in other neural crest cell lineages has not been investigated. In this study, we characterized NCC phenotypes in mutant zebrafish. We show that loss of Her9 perturbs the development of several NCC derivatives. mutants display a variety of NCC defects, including craniofacial abnormalities, alterations in pigment cell lineages, and improper formation of the gut. These phenotypes are associated with defects in neural crest cell specification, migration, and differentiation, as well as an upregulation in expression of BMP ligand genes. Furthermore, loss of Her9 leads to apoptosis of NCC derivatives. Collectively, our results show that Her9 functions in neural crest development by regulating members of the NCC gene regulatory network (GRN) to control NCC specification, migration, differentiation and survival.