Based on the previous genetic map of the yellow seed color gene,the sequences of Brassica rapa and Arabidopsis genomes were employed to design primers.Five primer pairs were from a B.rapa BAC clone KBrH105I15 and six pairs of IP primers were based on a sequence between At3g14120 and At3g29615 in Arabidopsis chromosome 3,which is a homologous region of yellow seed color gene.These 11 pairs of primers were used to amplify an F₂ population consisting of 1 212 individuals which from ‘Wuqi yellow-seeded’ and ‘Wugong brown-seeded’ mustard.As a result,Y12 from KBrH105I15 and IP-6 from At3g24180 were linked to the yellow seed color gene tightly,and Y12 was a co-dominant marker.These two markers were located on either side of the target gene at a distance of 0.2 and 0.1 cM.The genetic distances were shortened by 0.3 and 0.2 cM,respectively compared to the closest markers reported previously.The development of these two closer markers laid a good foundation for cloning the yellow seed color gene from yellow-seeded mustard.