Abstract: To analysis the genetic diversity of 90 germplasm, ISSR and SRAP markers were studied by polymorphisms, genetic diversity, genetic distance and cluster analysis.Our results showed that the total number of amplified bands, the average number of amplified bands and the average number of polymorphic bands obtained from SRAP marker are more than those marked by ISSR, and the range of genetic distance marked by SRAP was broader.However, there had no difference of the polymorphism ratios of the two markers.Furthermore, there had 52% variations between the populations and nearly 48% variations in populations, suggesting that the two markers are similar in genetic diversity analysis.Cluster analysis marked by ISSR showed that the dioscorea resources are classified into 4groups with a genetic distance of 0.13, and the results marked from SRAP showed that they are classified into 5 groups with a genetic distance of 0.18.In conclusion, our results suggest that SRAP marker is more suitable for the analysis on the genetic diversity of dioscoreae.