Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum, is an important disease of oilseed brassicas, yet the susceptibility of Australian varieties is unknown. Fifty-five historic, current and potential new Australian canola and mustard varieties were field-screened to determine their relative levels of resistance to SSR. Mean lesion length following stem inoculation with a highly virulent isolate (MBRS1) of the prevailing S. sclerotiorum pathotype (76) ranged from 3.0 mm in the B. napus cultivar Mystic to 202.6 mm (P < 0.001). Three recently developed B. juncea varieties or breeding lines, Sahara, JB0T-908982 and Xceed X121 CL, were extremely susceptible to S. sclerotiorum (mean lesion lengths 90.6, 132.3 and 202.6 mm, respectively). Histological study showed that the high level of resistance in Mystic was associated with strong deposition of lignin in stem cortical cell walls to form a barrier between the invading pathogen and the vascular tissues. Lack of association between mean lesion length and the year of varietal release (R² = 0.005) shows that there has been no improvement in level of resistance to SSR in Australian canola and mustard varieties over the last two decades. Although the very high susceptibility of a few B. juncea varieties demonstrated the value of SSR resistance present in B. napus varieties, this level of resistance is inadequate to prevent ongoing, severe yield losses from SSR under conditions conducive for disease development. Breeding programs can immediately utilise the SSR resistance in Mystic, and other recently identified resistances. This will enable a shift from the current dependence on fungicidal control to reliance on cost-effective, sustainable host resistance as the basis for better management of SSR.