The development of yellow-seeded varieties of Brassica napus for improving the oilseed quality characteristics of lower fiber content and higher protein and oil content has been a major focus of breeding researches worldwide in recent years. With the black-seeded 'Youyan 2' as male and the yellow-seeded GH06 as female parents respectively, F2 population of 132 individuals were obtained. A linkage map was constructed with 164 markers including 125 AFLP, 37 SSR, 1 RAPD and 1 SCAR markers distributed over 19 linkage groups covering approximately 2 549.8 cM with an average spacing of 15.55 cM. Two loci located on the 5th and 19th group were detected for the trait of seed coat color based on the linkage group using multiple interval mapping method and explained 46% and 30.9% of the phenotypic variation, respectively.