OBJECTIVE: The nucleoporin NUP98 is a component of the nuclear pore complex which regulates nucleo-cytoplasmic trafficking. It has been characterized in acute myeloid leukemia as a fusion partner during chromosomal translocation. In this study, we identified a zebrafish nup98 gene and examined its role in embryonic development. METHODS: Two expressed sequence tags with translated sequences homologous to human NUP98 were identified. The gene was cloned by PCR from cDNA of zebrafish embryos. Cellular functions of zebrafish NUP98 were investigated in HeLa cells. nup98 expression and developmental functions in zebrafish embryos were investigated by whole-mount in-situ hybridization and morpholino knockdown. RESULTS: Protein sequence of zebrafish nup98 shared 65% identity to its human homolog. Ectopic expression of zebrafish nup98 rescued the defective mRNA export due to human NUP98 knockdown in HeLa cells. In zebrafish embryos, nup98 was expressed diffusely in eyes and the developing brain since 18 hpf. Knockdown of nup98 with morpholino upregulated pu.1 expression by 39+/-15% (p=0.0153) and scl expression by 36+/-7.6% (p=0.0017). Expression of genes associated with erythropoiesis was unchanged. The morphants also developed intracranial hemorrhage at 48 hpf due to defective blood vessel development. CONCLUSION: A novel zebrafish nup98 was identified and it serves a similar role in nucleo-cytoplasmic trafficking as human NUP98. During development, it modulates hematopoietic stem cell and early myeloid development and maintains the integrity of cranial vasculature in the developing central nervous system.