The cordon-bleu (Cobl) gene is widely conserved in vertebrates, with developmentally regulated axial and epithelial expression in mouse and chick embryos. In vitro, Cobl can bind monomeric actin and nucleate formation of unbranched actin filaments, while in cultured cells it can modulate the actin cytoskeleton. However, an essential role for Cobl in vivo has yet to be determined. We have used zebrafish as a model to assess the requirements for Cobl in embryogenesis. We find that cobl shows enriched expression in ciliated epithelial tissues during zebrafish organogenesis. Cobl protein is enriched in the apical domain of ciliated cells, in close proximity to the apical actin cap. Reduction of Cobl by antisense morpholinos reveals an essential role in development of motile cilia in organs such as Kupffer's vesicle and the pronephros. In Kupffer's vesicle, the reduction in Cobl coincides with a reduction in the amount of apical F-actin. Thus, Cobl represents a molecular activity that couples developmental patterning signals with local intracellular cytoskeletal dynamics to support morphogenesis of motile cilia.