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Brassica juncea (AABB) is a natural allopolyploid of Brassica rapa (AA) and Brassica nigra (BB). B. juncea group contains both oilseed types and vegetable types. Extensive phenotypic and molecular marker-based studies on oilseed types of B. juncea have identified two major divergent gene pools, the Indian gene pool and the east European gene pool. Hybrids between the lines of these two gene pools are heterotic for yield, and such hybrids have now been commercialized in India. The two gene pools are significantly contrasting in major agronomic traits like seed size, pod size, pod number, height and oil content. A major future challenge in heterosis breeding is to transfer superior traits from one gene pool to the other while retaining the overall genetic divergence. This would allow further increases in yield. Recent work has provided reasonable number of markers for molecular tagging of both qualitative and quantitative traits and comparative mapping with model crucifer Arabidopsis and other Brassica species. Current work involves development of “00” canola-quality lines and their agronomic trials, disease resistance and QTL introgression. As the crop holds great promise for dryland agriculture in India and many other such areas around the globe, a concerted international effort is required on germplasm exchange, genetics, genomics and breeding of B. juncea.