Cationic antimicrobial peptides (CAPs), which are part of innate defense mechanisms across the living kingdoms, have shown great potential in fighting against a broad spectrum of phytopathogens. Synthetic versions have been modeled on these natural peptides to incorporate desirable properties for use in agriculture. MsrA1 is a one such synthetic chimera of cecropin A and melittin CAPs with demonstrated antimicrobial properties. Here we describe the generation of transgenic Brassica juncea plants overexpressing the msrA1 gene with an aim of conferring resistance against fungal pathogens. Different transgenic lines were generated and characterized for integration and expression of the transgene. Five independent transgenic lines were evaluated for their resistance to Alternaria brassicae and Sclerotinia sclerotiorum, two of the most dreaded fungal pathogens that often devastate B. juncea crops. In vitro assays showed inhibition by MsrA1 of Alternaria hyphae growth by 44-62%. As assessed by the number and size of lesions and the time taken for complete leaf necrosis, the Alternaria infection in the potted plants was delayed and restricted in the transgenic plants in comparison to the untransformed control plants. The disease protection against this pathogen varied from 68.8-85% in different transgenic lines. Similar results were obtained with S. sclerotiorium infection. Whereas the lesions were more severe and spread profusely in the untransformed control plants the transgenic plants resisted the infection. Number of sclerotia formed in the stem of untransformed control plants were significantly more and larger in size than those present in the transgenic plants. The disease protection was estimated to be 56-71.5 %. Herein, we discussed the potential of engineering broad spectrum biotic stress tolerance by transgenic expression of CAPs in crop plants.