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<p>Abstract</p> <p>Background</p> <p>The Multinational <it>Brassica rapa </it>Genome Sequencing Project (BrGSP) has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for <it>Brassica rapa</it>. An integrated linkage map between the amphidiploid <it>B. napus </it>and diploid <it>B. rapa </it>will facilitate the rapid transfer of these valuable resources from <it>B. rapa </it>to <it>B. napus </it>(Oilseed rape, Canola).</p> <p>Results</p> <p>In this study, we identified over 23,000 simple sequence repeats (SSRs) from 536 sequenced BACs. 890 SSR markers (designated as BrGMS) were developed and used for the construction of an integrated linkage map for the A genome in <it>B. rapa </it>and <it>B. napus</it>. Two hundred and nineteen BrGMS markers were integrated to an existing <it>B. napus </it>linkage map (BnaNZDH). Among these mapped BrGMS markers, 168 were only distributed on the A genome linkage groups (LGs), 18 distrubuted both on the A and C genome LGs, and 33 only distributed on the C genome LGs. Most of the A genome LGs in <it>B. napus </it>were collinear with the homoeologous LGs in <it>B. rapa</it>, although minor inversions or rearrangements occurred on A2 and A9. The mapping of these BAC-specific SSR markers enabled assignment of 161 sequenced <it>B. rapa </it>BACs, as well as the associated BAC contigs to the A genome LGs of <it>B. napus</it>.</p> <p>Conclusion</p> <p>The genetic mapping of SSR markers derived from sequenced BACs in <it>B. rapa </it>enabled direct links to be established between the <it>B. napus </it>linkage map and a <it>B. rapa </it>physical map, and thus the assignment of <it>B. rapa </it>BACs and the associated BAC contigs to the <it>B. napus </it>linkage map. This integrated genetic linkage map will facilitate exploitation of the <it>B. rapa </it>annotated genomic resources for gene tagging and map-based cloning in <it>B. napus</it>, and for comparative analysis of the A genome within <it>Brassica </it>species.</p>