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High-throughput genomics technologies today offer unprecedented possibilities for gene discovery, complex trait analysis by genome-wide association studies, global gene expression analyses, genomic selection and predictive breeding strategies. Dissection of the complex Brassica napus genome using mapping-by-sequencing techniques provides a powerful bridge between genetic maps and genome sequences. The completed sequence of the Brassica rapa A genome and the expected forthcoming publication of the C genome (Brassica oleracea) will greatly accelerate the release of public reference sequences for B. napus (genome AC). Dramatically falling DNA costs for targeted or genomic resequencing and the availability of a new, high-density B. napus single-nucleotide polymorphism (SNP) array open the way for considerably more efficient mining and exploitation of genetic variation within the primary and secondary gene pools of B. napus. In this review, we outline some of the most significant recent advances in high-throughput genomics of Brassica crops and their potential impact on germplasm development and breeding of oilseed rape and canola in the coming years and decades.