With the objective of identifying molecular markers for the seed oil content in mustard (Brassica juncea), which is known to be quantitatively inherited, 94 F6 generation recombinant inbred lines (RILs) developed from an intervarietal cross (Varuna × BEC144), were characterised. Oil content, determined by pulsed nuclear magnetic resonance technique, varied from 25.7% to 52.3% among the RILs. The frequency distribution of the trait was normal with mean 39.24 and standard deviation 4.52. Bulked segregant analysis of the RILs enabled fast and efficient screening of 219 random decamer primers for identification of informative primers. Single factor analysis of variance revealed significant association of oil content with three RAPD markers, viz., OPH111350, OPJ061200 and OPL05600 which individually explained 6% of the trait variance. Molecular data indicated dispersion of desirable quantitative trait loci in the two parent varieties.