Notch genes encode transmembrane receptors that interact with numerous signal transduction pathways and are essential for animal development. To facilitate analysis of vertebrate Notch gene function, we isolated cDNA fragments of three novel Notch genes from zebrafish (Danio rerio), Notch1b, Notch5 and Notch6. Notch1b is a second zebrafish Notch1 gene. From analysis of the Notch1b sequence we argue that the various vertebrate Notch gene subfamilies encode receptors with different signalling specificities. Notch5 and Notch6 represent novel vertebrate Notch gene subfamilies. Remarkably, Notch1b lacks expression in presomitic mesoderm, Notch5 is expressed in a metameric pattern within the presomitic mesoderm whilst Notch6 expression is excluded from the nervous system. The expression patterns of these genes suggest important roles in gastrulation, somitogenesis, tail bud extension, myogenesis, heart development and neurogenesis. We discuss the implications of our observations for Notch gene evolution and function.