A genetic map of B. juncea was used to localize genes and QTLs for a number of seed quality traits in this species. The map was constructed using a segregating population of 119 F-1 microspore derived doubled haploid (DH) lines from a cross between a high oil B. juncea breeding line of AAFC Saskatoon (derived from a high oil Russian line) and an adapted canola quality B. juncea line. The map consists of 343 RFLP markers distributed in 18 linkage groups and five short unassigned segments covering a distance of 2073 cM. The seed quality traits concerning contents of oil, erucic acid, linolenic acid, total alkenyl glucosinolates and individual classes of alkenyl glucosinolates of the mapping population were evaluated by field trials for two years. The data were analyzed using a QTL-interval mapping approach. The locations of the QTLs on the map for these traits are presented, and the implications on the development of marker-assisted selection for some of these traits are discussed.