AFLP, i.e., Amplified fragment length polymorphism, is a newly developed molecular marker by Zabeau and Vos P in 1992. This marker combining the characters of RFLP and RAPD marker, it not only has the reliability of RFLP but also has the efficiency of RAPD. This paper introduces the basic principle, technical protocol and improving methods of AFLP marker, presents its application in the Population Biology, Conservation Biology, Molecular Systematic nowadays and forecasts its develop outlook.