Abstract:RAPD assessment on genetic variations of 16 mustard ( Brassica juncea Coss. ) varieties were carried out. 27 primers were screened from sixty 10 bp arbitrary primers, and a total of 336 DNA bands were amplified, among which 275 (81.85 % ) were polymorphic. The average number of DNA band amplified by each primer was 12.44, and the average genetic distance among 16 mustard varieties was 7.34. Based on UPGA cluster analysis of 240 DNA hands amplified by 19 primers, a DNA molecular dendmgram was established for 16 vegetable mustard varieties in China, which divided the 16 mustard varieties into three groups: group A, B and C. Group A included seven varieties, group B eight and group C only one. Group B could be divided into two subgroups:Bi and Be. The molecular foundation of genetic diversity of mustard was explored.