To analyse the genetic diversity and relationship of Asarum germplasm resources, sixty-one Asarum germplasm were tested using ISSR and SRAP Markers. The results were as follows: (1) The average of bands amplified per primer by ISSR and SRAP was 8.35 and 7.85 respectively. The percentage of polymorphic bands of ISSR and SRAP was 86.3% and 86.0% respectively. (2) The percentage of polymorphic bands of ISSR was higher than those of SRAP amplified using same number of primers. (3) According to the dendrogram of cluster analysis, all the accessions could be classified clearly. The cluster of accessions was associated with resource region. Comparing to ISSR, SRAP marker had the advantage in reflecting the difference of genome. (4) Asarum heterotropoides Fr. Var. mandshuricum (Maxim) kitag. and Asarum sieboldii Miq. var. seoulense Nakai from same origin clustered first in two clustering dendrogram which showed they have close genetic relationship. (5) Not all A. heterotropoides or A. sieboldii were clustered together, and this showed that the taxonomy according to molecular marker was inconsistent with plant characteristics.