A fragment of hedgehog was first isolated by polymerase chain reaction (PCR) from genomic DNA of Qingdao amphioxus using degenerate primers designed according to the conserved sequence in the second exon of hedgehog family. Then RT-PCR and rapid amplification of cDNA ends (3′ and 5′ RACE) were carried out using the mRNA of 18-h neurulae as template. The PCR products were sequenced and constituted a 3540 bp-long hedgehog gene, containing a complete open reading frame. The predicted protein is 415-amino-acids long, showing a high level of identity to other hedgehog proteins. The results show that Qingdao amphioxus contains one and probably only one hedgehog gene. Whole mount in situ hybridization revealed that hedgehog expressed in the prospective notochord, the notochord, floor plate of neural tube and mouth, similarly to its vertebrate homologue Sonic-hedgehog gene. This suggested that amphioxus hedgehog gene might function in the notochord induction to neural tube cells and in the development of the mouth.