Rapeseed (Brassica napus L.) is an important source of edible vegetable oil and feed protein; however, seed pigments affect the quality of rapeseed oil and the feed value of the residue from oil pressing.  Here, we used a population of rapeseed recombinant inbred lines (RILs) derived from the black-seeded male parent cultivar Zhongyou 821 and the yellow-seeded female parent line GH06 to map candidate genes controlling seed pigments in embryos and the seed coat.  We detected 94 quantitative trait loci (QTLs) for seed pigments (44 for embryos and 50 for seed coat), distributed over 15 of the 19 rapeseed chromosomes.  These included 28 QTLs for anthocyanidin content, explaining 2.41–44.66% of phenotypic variation; 24 QTLs for flavonoid content, explaining 2.41–20.26% of phenotypic variation; 16 QTLs for total phenol content, accounting for 2.74–23.68% of phenotypic variation; and 26 QTLs for melanin content, accounting for 2.37–24.82% of phenotypic variation, indicating that these traits are under multigenic control.  Consensus regions on chromosomes A06, A09 and C08 were associated with multiple seed pigment traits, including 15, 19 and 10 QTLs, respectively, most of which were major QTLs explaining >10% of the phenotypic variation.  Based on the annotation of the B. napus “Darmor-bzh” reference genome, 67 candidate genes were predicted from these consensus QTLs regions, and 12 candidate genes were identified as potentially involved in pigment accumulation by RNA-seq and qRT-PCR analysis.  These preliminary results provide insight into the genetic architecture of pigment biosynthesis and lay a foundation for exploring the molecular mechanisms underlying seed coat color in B. napus.