This study identified the mutated sill gene, which is responsible for the nbb phenotype. sill gene is located on 22 chromosome and encodes 1263 amino acids. The function of sill is unclear in zebrafish. Using the gene candidate cloning approach, we identified a 'G->A' site mutation in the sill transcript, resulting in a truncated sill protein. RT-PCR and in situ hybridization results demonstrated that sill expresses in the very early stages of embryonic development and expresses in many different cell types. In addition, the relationship between sill and shh pathway was examined. We found that the expression of the shh pathway target gene gli1, which play a role in inducing ventral neural tube development, was decreased in nbb mutants. To further investigate the nbb phenotype, we also examined the development of TN in nbb mutants and forskolin treated fish.The data suggested that nbb phenotype was caused by the mutated sill, inducing deficiencies in the shh signaling pathway. Additionally, abnormal development of the TN caused by deficient shh pathway may also contribute to the nbb phenotype during the early embryonic development.