Abstract: By taking 30 samples of Coix species as testing materials， the genetic diversity and genetic relationship was analyzed using AFLP molecular markers technology. The optimal analysis system of AFLP has been established by studying the key factors of conventional process such as gene extraction， restriction digestion and link up， pre-amplication， selective amplification， electrophoresis and siliver staining detection. The result showed that the genome DNA was digested more completely by using two-step method compared with one-step method. In each step， the enzyme reaction time was 4 h added with 15 min for enzyme inactivation. The connection product should be diluted for 10 times and the pre-amplification product should be diluted for 50 times to get a better result. With application of the established system， 14 selective amplification primers with better polymorphism were selected out from 64 primers.

Key words: Coix, molecular markers, AFLP system