Both Alternaria japonica and A. brassicae cause severe Alternaria leaf spot on canola (Brassica napus) and mustard (B. juncea). We tested 103 Brassicaceae varieties including 93 Australian canola, nine Indian mustard, and a single variety of Ethiopian mustard (B. carinata) under greenhouse conditions to identify host resistance to Alternaria leaf spot caused by A. japonica and A. brassicae in terms of disease incidence (percentage leaf disease incidence, %LDI), disease severity (percentage leaf area diseased, %LAD) and defoliation (percentage leaf collapse index, %LCI). Against A. japonica, across the three parameters, B. napus Surpass 404 CL was the most resistant (%LDI 7.5, %LAD 5.0, %LCI 0). Varieties Hyola 635 CC, Oscar, AG-Outback and Rottnest, with %LDI 15.6–19.4 and %LAD 12.5–15.6, also showed strong resistance, and with %LCI 10. Varieties 47C02, ATR-Signal and Clancy of B. napus showed a moderate level of resistance across %LDI (21.2–25.6) and %LAD (15.0–20.6), along with a low level of defoliation (%LCI 10). Varieties 46C03, 46C72, ATR-Cobbler and Granite TT of B. napus also showed a moderate level of resistance, with %LDI 23.1–28.7, %LAD 18.1–20.6 and %LCI 11.2–14.4. The significance of this resistance against A. japonica is highlighted by the severe disease on B. napus Thunder TT (%LDI 78.8, %LAD 72.5, %LCI 47.5). Against A. brassicae, all varieties showed susceptibility; however, B. napus ATR-Grace was the least susceptible in relation to disease incidence (%LDI 41.2) and severity (%LAD 36.2), and B. napus Hyola 450 TT the most susceptible (%LDI 90.0, %LAD 82.5). Variety Hurricane of B. napus was the least susceptible in terms of consequent defoliation (%LCI 11.2) and B. napus CBTM Tribune the most susceptible (%LCI 81.2). The B. carinata variety BCA 1 (ATC 95065) and all test B. juncea varieties showed susceptibility to both pathogens. These findings demonstrate high levels of resistance across Australian canola varieties against A. japonica that can be directly deployed where A. japonica is important and can be utilised by breeders for improving resistance in future varieties. By contrast, susceptibility across Australian canola and mustard varieties to A. brassicae is concerning, highlighting a need to locate suitable resistances and, until effective host resistance can be located, to develop and deploy cultural and chemical options.