Important fungal , bacterial and viral diseases affect Brassica juncea (Indian mustard). Here, a comprehensive genome-w ide analysis of disease resistance (A) genes (nucleotide-binding site-leucine-rich repeat, receptor-like kinases and receptor-like proteins) was performed in B. juncea. This provides an important resource to identify candidate genes for specific diseases, a key step to enhancing resistance against important pathogens. Candidate A genes we re identified that were located within published disease loci. SNPs identified within the candidate genes can be used for downstream analysis, such as marker assisted selection and to validate candidate genes for breeding improved B. juncea cultivars.