For conservation and utilization of Akebia trifoliata resources scientifically in Guizhou, we chose two kinds of method called AFLP and ISSR markers to analysis the genetic relationship and genetic diversity about A. trifoliata with total of 31samples. They came from part of the county or city in Guizhou Province. The results showed that: (1) with 8 pairs of primer we gained 9 252 and 11 643 amplification DNA bands, respectively，The polymorphism rates are 95.31% and 100%, respectively, meaning that the germplasm diversity is abundant in tested samples. (2) For AFLP and ISSR, the ranges of similarity coefficient are between 0.762 3 to 0.893 5 and 0.828 9 to 0.917 1 respectively, showing that the resources of A. trifoliata has a certain genetic differences between different species in Guizhou. (3) Clustering analysis told us, in the similarity coefficient of 0.85, 31 A. trifoliata resources were divided into 5 groups and 3 group, among them the No. 26, No.27, No.28, No.30 samples belong to the same group, as well as No.29 and No.31.Especially No.4, No.8 and No.26, No.27 may be the same source of germplasm，because they got the largest similarity coefficient in each other.