Using RIL population constructed from multiple crosses of Sichuan yellow seed inbred lines and purple leaf mustard inbred lines, the genetic maps of Brassica juncea were constructed with genetic analysis techniques. With anchoring BAC, 16 contigs containing 538 BACs were obtained. With reference to Brassica juncea genome, the obtained physical map was estimated to be 46.26 Mb. In comparison with reported genomes of Brassica rapa, Brassica napus, and Brassica juncea, insertions and deletions were found in A9 chromosomes of Brassica juncea.