The objective of this study was to compare the feasibility of using SRAP, ISSR and combination of the both in origin and evolution of jute (Corchorus L). Ninety-six jute genotypes were tested by these three methods. The results were as follows: (1) The percentage of polymorphic bands of SRAP was 100%, which was higher than that of 98.1% of ISSR, and the polymorphic bands amplified per primer by SRAP were also higher than these of ISSR. (2) On the dendrogram based on SRAP data, jute genotypes were close to be classified. The trend of origin and evolution of jute could be clarified. However, a few genotypes were misled to other taxonomic groups, which affected the accuracy of analysis on origin and evolution of jute. On the dendrogram based on ISSR data, many capsularis cultivars were found to be clustered together and could not be identified clearly, and also the time of origin was difficult to confirm. (3) Based on the dendrogram derived from SRAP and ISSR data, different taxonomic groups of jute were found to be clustered orderly, and the relationship of origin and the trend of evolution within jute genus manifested clearly. (4) The strategy of SRAP and ISSR combination was better than that of SRAP alone, and then followed by ISSR. Hence, the strategy of SRAP and ISSR combination should have priority in studies on the origin and evolution of jute.