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Brassica juncea (Indian mustard) is an economically important cultivated annual crop worldwide. However, there are a number of important diseases affecting B. juncea, including blackleg (Leptosphaeria maculans, L. biglobosa), sclerotinia stem rot (Sclerotinia sclerotiorum), white rust (Albugo candida), alternaria blight (Alternaria brassicae, A. brassicicola, A. raphani), downy mildew (Hyaloperonospora brassicae), white leaf spot (Neopseudocercosporella capsellae), clubroot (Plasmodiophora brassicae), powdery mildew (Erysiphe cruciferarum), Turnip yellows virus (formerly Beet western yellows virus), Cauliflower mosaic virus, Turnip mosaic virus, and leaf blight (Pseudomonas syringae). This paper reviews what is currently known about disease resistance in B. juncea, including the mechanism of resistance and molecular markers associated with disease resistance, that can be used to develop improved B. juncea cultivars through marker-assisted selection (MAS). It also highlights how MAS, phenotypic selection, and transgenics provide pathways to validate candidate genes as functional resistance genes and new resources for breeding programmes for elite B. juncea cultivars. In addition, this review of disease resistance in B. juncea, together with the release of the B. juncea genome, will guide further discovery and identification of resistance genes and consequent substantial improvement in crop protection.