The spermatogenesis associated 4 gene (SPATA4, previously named TSARG2) was first cloned in human tissues and was reported to be a candidate spermatocyte apoptosis-related gene that is expressed specifically in testis. Analysis of SPATA4 expression and regulation in zebra fish may provide insight into the understanding of the complicated process of gonadogenesis. In this study, we cloned and characterized the SPATA4 gene from zebra fish (Danio rerio), which is homologous to human and mouse SPATA4. Zebra fish SPATA4 consists of six exons separated by five introns, as all SPATA4 genes in vertebrates. A promoter region was predicted using homologous blast and cloned for further study, and possible transcription factors were analyzed in this region. The putative protein encoded by this gene was analyzed using bioinformatics methods. Multi-tissue RT-PCR results demonstrated that the zebra fish SPATA4 gene is expressed specifically in testis and slightly in ovary. Analysis of the SPATA4 sequence and its spatial expression pattern indicate that this gene is highly conserved and may play an important role in the process of zebra fish gonadogenesis.