Abstract: AFLP (amplified fragment length polymorphism) analysis system was established in research of Pearl River armorhead catfish, Cranoglanis bouderius. The several steps for AFLP analysis were examined, including DNA extraction, double-restriction endonuclease reaction, single-restriction endonuclease reaction, adadpter ligation reaction, preamplification reaction, selective amplification reaction and Ag-NORs reaction. The AFLP fingerprinting experiments of C.bouderius with primer combination, E+AAG/M+CTG and P+ATT/T+ACA, were performed, which had about 50 clear and bright amplification bands.