A new and efficient reaction system has been set up, in which the MseⅠ primers were fluorescent labeled for auto-sequencer. PCR reagents and primers and adapters of MseⅠ and EcoRⅠ, which were synthesized, the AFLP protocol has been modified, and reaction and electrophoresis conditions were optimized, the results obtained can be comparable to that of AFLP fluorescent labeled AFLP kits with less cost.