Pharyngeal arches are a prominent and critical feature of the developing vertebrate head. They constitute a series of bulges within which musculature and skeletal elements form; importantly, these tissues derive from different embryonic cell types [1]. Numerous studies have emphasised the role of the cranial neural crest, from which the skeletal components derive, in patterning the pharyngeal arches [2-4]. It has never been clear, however, whether all arch patterning is completely dependent on this cell type. Here, we show that pharyngeal arch formation is not coupled to the process of crest migration and, furthermore, that pharyngeal arches form, are regionalized and have a sense of identity even in the absence of the neural crest. Thus, vertebrate head morphogenesis can now be seen to be a more complex process than was previously believed and must result from an integration of both neural-crest-dependent and -independent patterning mechanisms. Our results also reflect the fact that the evolutionary origin of pharyngeal segmentation predates that of the neural crest, which is an exclusively vertebrate characteristic.