Sclerotinia rot caused by Sclerotinia sclerotiorum is a major constraint in mustard production. The present investigation evaluated the antagonistic potential of fungal and bacterial bioagents and their role in inducing biochemical defence responses in mustard cultivars RH-30 (Brassica juncea (L.) Czern.) and HC-212 (Brassica carinata A. Braun). The investigation was conducted through both in vitro and screenhouse experiments. A total of fifteen Trichoderma isolates and eleven bacterial antagonists were evaluated against S. sclerotiorum using dual culture assays to determine their antagonistic efficacy. The most effective fungal and bacterial isolates were subsequently characterised through internal transcribed spacer (ITS) and 16S ribosomal RNA (16S rRNA) gene sequencing respectively. Under screenhouse conditions, selected antagonists were assessed for their ability to induce systemic resistance by analysing antioxidant metabolites, oxidative stress markers, defence enzymes and stress-responsive proteins following pathogen inoculation. Among the fungal antagonists, isolate HHT recorded the highest mycelial growth inhibition (77.33 %), followed by HST-2 (75.19 %), HRoT (74.89 %). Among bacterial antagonists, HRBa-3 exhibited the maximum inhibition (69.29 %). Molecular characterisation identified HHT as Trichoderma asperellum and HRBa-3 as Bacillus subtilis. Antagonist treated plants showed significantly enhanced antioxidative and defence-related biochemical responses following pathogen challenge. The cultivar HC-212 exhibited higher accumulation of total phenolics, stress-responsive proteins and greater activity of defence enzymes, including catalase (CAT), superoxide dismutase (SOD), polyphenol oxidase (PPO), peroxidase (POX), phenylalanine ammonia-lyase (PAL) and tyrosine ammonia-lyase (TAL), than RH-30. Conversely, lower levels of oxidative stress indicators such as malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) were recorded, particularly under T. asperellum treatment. Correlation analysis revealed strong positive associations among biochemical defence markers, indicating a coordinated defence mechanism during pathogen stress. The study demonstrates that T. asperellum and B. subtilis are effective biocontrol agents capable of suppressing S. sclerotiorum and enhancing host defence mechanisms through induced systemic resistance. Therefore, these bioagents are recommended as environmentally sustainable components of integrated disease management strategies for the effective management of Sclerotinia stem rot in mustard.