Objectives:To help understand theepigenetic regulation of seed coat color in Brassica napus.Methods:Theyellow-seeded rapeseed line derived from the somatichybrids of B.napus–Sinapis alba and the black-seededrapeseed line were used as experimental materials.Methylation-sensitive amplification polymorphism(MSAP)analysis was performed to investigate the target regions of seed coat variation in B.napus.Polymorphic sequences with a methylationpattern that varied between yellow-and black-seededrapeseeds were determined.Changes in gene expression were assessed throughqRT-PCR to investigate the effects of DNA methylation on gene expression.Results:A totalof 760 fragments were amplified by 45 primer pairs.In these fragments,10%of demethylation and 5%of hypermethylation were detected in yellow rapeseeds compared with black rapeseeds.A total of 35 fragments with different DNA methylation ordemethylation patterns between the yellow-andblack-seeded rapeseed were cloned and sequenced.Thegene expression of the demethylated fragments in theyellow rapeseeds was upregulated.For instance,bHLH,a transcription factor regulating flavonoidbiosynthesis,was upregulated at 3–5 weeks afterflowering of yellow seeds.Conclusions:In ourstudy,DNA methylation changes between the developingseeds of yellow-and black-seeded B.napus,and the total methylation in yellowrapeseeds was lower than that in black seeds.These methylation changes were probably correlated with seed coatvariation.Therefore,epigeneticchanges among rapeseed lines with different seedcolors help elucidate the formation of the yellow seedcharacter.