Abstract: 【Objective】Rapeseed(B.juncea L.) local germplasm resources would be conserved and utilized in rapeseed breeding more effectively, the genetic diversity in them was studied on molecular level instead of apparent genetics level. 【Method】73 resources in B.juncea L. from Sichuan or other regions were selected, the genetic relationship among them was studied using RAPD marker cluster analyzing and botanical trait cluster analyzing. 119 RAPD primers were used and 25 main botanical traits or 88 trait grades genetic stably were observed.【Results】The tested resources were divided into three groups and 13 units in the RAPD marker cluster analyzing. Qiubeiheiyoucai from Yunnan was the first group, more likely a special original resource. The majority resources in the second group were come from Yunnan. The majority resources in the third group were come from Sichuan(including Chongqing). The second group was divided into two sub-groups. The majority resources in one were come from Guizhou and the majority resources in the other were come from Guizhou and Yunnan. The third group were also divided into two sub-groups. The majority resources in one were come from the regions out of Sichuan and the majority resources in the other were come from Sichuan. The tested resources were divided into six groups and 28 units in the botanical trait cluster analyzing. The resources in the first group were come from Sichuan(including Chongqing). The resources in the second group were come from Sichuan and Guizhou. The majority resources in the third group were come from Yunnan-Guizhou plateau and Qinghai-Xizang plateau. The majority resources in the fourth group were come from Liangshan region in Sichuan and Yunnan-Guizhou plateau. B.carinata L. come from Ethiopia and Changningbendihuangyoucai come from Sichuan were the fifth group. The majority resources in the sixth group were come from Eastern Sichuan, Liangshan region in Sichuan and Yunnan-Guizhou plateau.【Conclusion】The different between resources in B.juncea L. from Sichuan and from Yunnan,Guizhou and other regions was obvious. There was abundant genetic diversity in resources in B.juncea L. from Sichuan. The genetic relationship among resources from different ecological regions or resources from the same ecological regions was near or far, decided by the specific ecological environment and the behavior of human. The genetic relationship and the genetic distance could be identified by RAPD marker cluster analyzing or botanical trait cluster analyzing. But the results from RAPD marker cluster analyzing were more reliable.