The NR5A family of orphan nuclear receptors has been implicated in development of the vertebrate embryo, but their exact role remains largely unknown. To evaluate the regulation and developmental role for ff1a (NR5A2) in zebrafish (Danio rerio), we performed morpholino knockdown to block translation of the ff1a gene and the upstream located sox9a gene during embryogenesis. Using a newly developed antibody against Ff1a we could show that the ff1a morpholinos were functional and that a reduction in the expression of Ff1a correlated to altered phenotypes. The role of Sox9a in ff1a gene regulation and function was studied using sox9a morpholinos. Knock-down of sox9a resulted in abolished ff1a signals in the somites, mandibular arches and pharyngeal arches, while the pectoral fin signal remained. The reduction in Ff1a levels correlated to truncated tails and cranio-facial malformation. As Sox9a is involved in chondrocyte development we analysed for cartilage formation and found that blocking translation of either sox9a or ff1a also blocked cartilage formation. In light of the results, the present study suggests a novel function of ff1a in chondrocyte development.