A genetic linkage map of mustard (Brassica juncea) was developed using two double haploid populations produced from crosses between a low erucic cultivar “ZEM1” and two moderate erucic acid lines “Vniimk351” and “Vniimk405” with the use of SSR and SRAP markers. The linkage map of the ZEM1xVniimk351 population included 13 linkage groups with an overall length of 791 cM with an average marker interval of 5.7 cM. The linkage map of the ZEM1xVniimk405 population also contained 13 linkage groups with a distance of 623 cM and an average marker interval of 4.6 cM. Using the linkage maps for the two populations, QTLs were detected for seed oil, protein and fatty acids. QTL analysis for fatty acids indentified QTLs on LG1, 7 and 12 for the ZEM1xVniimk351 population and LG1, 3 and 4 for the ZEM1xVniimk405 population. Analysis for the seed oil and protein content in the ZEM1xVniimk351 population identified 2 QTLs on LG1 and LG4 and 1 QTL on LG1 respectively. The QTL analysis ZEM1xVniimk405 of oil and protein content identified 1 QTL for oil and protein on LG1. The variation of fatty acids was shown to be the result of monogenic inheritance of the FAE1 gene in both populations.