The hindbrain (brainstem) of all vertebrates follows a segmental developmental strategy and has been the focus of intense study not only for its intrinsic interest but also as a model for how more complex regions of the brain are patterned. Segmentation ultimately serves to organize the development of neuronal populations and their projections, and regional diversity is achieved through each segment having its own identity. The latter being established through differential expression of a hierarchy of transcription factors, including Hox genes, Krox20, and Kreisler/Valentino. Here we identify a novel signaling center in the zebrafish embryo that arises prior to establishment of segmental patterning and which is located centrally within the hindbrain territory in a region that corresponds to the presumptive rhombomere 4. We show that signaling from this region by two members of the FGF family of secreted proteins, FGF3 and FGF8, is required to establish correct segmental identity throughout the hindbrain and for subsequent neuronal development. Spatiotemporal studies of Fgf expression suggest that this patterning mechanism is conserved during hindbrain development in other vertebrate classes.