The whole process of the knowledge discovery based on the bioinformatics has been showed by the example of gene cloning of Siniperca chuatsi. The gene information of related fishes are got from the nuclei acid databases of GenBank, EMBL and the fish databases using the retrieval tools of Entrez and SRS. The arithmetic method of half experience value has been adopted. The methods of BLAST and FASTA are combined with the classification database of Taxonomy. The adequacy filtration programs are selected to filtrate the inefficacy data. Finally, the knowledge consistent with expect result of knowledge discovery are got.