A morphologically different, perennial and highly pungent Capsicum cultivar ‘Dalle Khursani’ is available in the Darjeeling district of West Bengal over many decades. Its counterpart in Sikkim was identified as polyploid Capsicum cultivar with 2n = 4x = 48 chromosomes. However, cytogenetical status of the cultivar growing in West Bengal was lacking. The present study has carried out extensive morphological, chromosomal and molecular analysis on seven ‘Dalle Khursani’ populations of West Bengal. Our results on flower morphology explicitly delimit ‘Dalle Khursani’ populations from the members of ‘C. annuum complex’. Somatic and gametic chromosome analysis has clearly established their polyploid chromosome number 4x = 48 and allopolyploid nature of the cultivar (2n = 4x = 48). Fluorescent banding analysis with CMA revealed CMA + ve/DAPI-ve heterochromatin blocks in four ‘Dalle Khursani’ populations for the first time indicating the prevalence of GC rich heterochromatin in the studied taxon. RAPD based genomic DNA analysis has exhibited similar banding profile within the populations and their complete difference from the diploid members of ‘C. annuum complex’. Our present studies in conformity with our earlier report have firmly established that allopolyploidy in Capsicum is not a rarity. It is available in Indian states and will help the Capsicum researchers and breeders in their future crop improvement programmes. © 2016 Elsevier B.V.