‘Dalle Khursani’ a highly pungent Capsicum is primarily cultivated for decades in the hilly region of North Eastern Himalayan States. All the studied ‘Dalle Khursani’ populations were found to be polyploid with 2n = 48 chromosomes. Allopolyploid nature of Dalle Khursani populations was revealed by gametic chromosome analysis. EMA method was used for chromosome analysis. Fluorescence banding revealed CMA + ve DAPI-ve bands were associated with nucleolar chromosomes. Genomic DNA analysis within the populations revealed their homology.