Pinin (pnn), a nuclear and desmosome-associated SR-like protein, has been shown to play multiple roles in cell adhesion, transcriptional regulation, pre-mRNA splicing and mRNA export. Because of the embryonic lethality of pnn-deficient mice, here we used the zebrafish system to investigate the functions of pnn. Injection of morpholinos into zebrafish to knockdown pnn resulted in several obvious defective phenotypes, such as short body, bent tail, and an abnormal pigment distribution pattern. Moreover, aberrant blood vessels were formed, and most of the cartilages of pharyngeal arches 3-7 were reduced or absent in pnn morphants. Because most of the defects manifested by pnn morphants were reminiscent of those caused by neural crest-derived malformation, we investigated the effects of pnn deficiency in the development of neural crest cells. Neural crest induction and specification were not hindered in pnn morphants, as revealed by normal expression of early crest gene, sox10. However, the morphants failed to express the pre-chondrogenic gene, sox9a, in cells populating the posterior pharyngeal arches. The reduction of chondrogenic precursors resulted from inhibition of proliferation of neural crest cells, but not from cellular apoptosis or premature differentiation in pnn morphants. These data demonstrate that pnn is essential for the maintenance of subsets of neural crest cells, and that in zebrafish proper cranial neural crest proliferation and differentiation are dependent on pnn expression.