Brassica juncea(AABB), Indian mustard, is a source of disease resistance genes for a wide range of pathogens. The availability of reference genome sequences forB. junceahas made it possible to characterise the genomic structure and distribution of these disease resistance genes. Potentially functional disease resistance genes can be identified by co-localization with genetically mapped disease resistance quantitative trait loci (QTL). Here we identify and characterise disease resistance gene analogs (RGAs), including nucleotide-binding site–leucine-rich repeat (NLR), receptor-like kinase (RLK) and receptor-like protein (RLP) classes, and investigate their association with disease resistance QTL intervals. The molecular genetic marker sequences for four white rust (Albugo candida) disease resistance QTL, six blackleg (Leptosphaeria maculans) disease resistance QTL andBjCHI1, a gene cloned fromB. junceafor hypocotyl rot disease, were extracted from previously published studies and used to compare with candidate RGAs. Our results highlight the complications for the identification of functional resistance genes, including the duplicated appearance of genetic markers for several resistance loci, includingAc2(t), AcB1-A4.1, AcB1-A5.1,Rlm6andPhR2in both the A and B genomes, due to the presence of homoeologous regions. Furthermore, the white rust loci,Ac2(t)and AcB1-A4.1, mapped to the same position on chromosome A04 and may be different alleles of the same gene. Despite these challenges, a total of nine candidate genomic regions hosting 14 RLPs, 28 NLRs and 115 RLKs were identified. This study facilitates the mapping and cloning of functional resistance genes for applications in crop improvement programs.Supplementary InformationThe online version contains supplementary material available at 10.1007/s11032-022-01309-5.