Abstract: Totally 28 EcoR I/Mse I AFLP selective primer pairs and 64 Pst I /Taq I AFLP selective primer pairs were used in the analysis of 2 peanut mapping parental lines and their F1 hybrid. The NPAR1WAY procedure was conducted using the SAS System for Windows 6.12 package. The results showed significant difference（at 0.01 level）between enzyme combinations in the number of polymorphic bands and polymorphic percentage，and no significant difference in total number of bands，on a per primer pair basis. The study demonstrated that resorting to alternative enzyme combinations may be judicious options in disclosing the genetic variations in the cultivated peanut.