The North Eastern Himalayan (NEH) regions of India are considered as one of the major repositories of the “Capsicum annuum complex” which comprises of three cultivated species namely C. annuum, C. frutescens, and C. chinense. The interspecific delimitation within this large complex is ill-defined due to poorly developed crossing barriers and lack of discontinuous morphological characters. The present study elucidates the relationship among nine different cultivars of three Capsicum species on the basis of floral morphology and karyological parameters for the first time. Different floral characteristics such as margins and constrictions of calyx, type of pedicel, flower size, and color were found to have paramount importance in the species delimitation within the studied members of “C. annuum complex.” The present karyomorphometric study explicitly revealed differences between the observed chromosomal data such as karyotype formulae, ordering of satellite bearing chromosome pairs and total diploid chromatin length which aid in resolving interspecific relationship among the studied cultivars of Capsicum. The present analyses unambiguously distinguished all cultivars of C. annuum from the members of C. frutescens and C. chinense and also proposed that among the five cultivars of C. annuum, Ghee lanka was comparatively distant from the other four cultivars on the basis of their karyomorphological characteristics. For the first time karyotype of hottest Indian chili is included in this paper. Comprehensive knowledge on floral morphology and karyotypes of some Himalayan Capsicums not only help to conserve genetic diversity but also help capsicum breeders for their basic and applied research. © 2016, Springer-Verlag Wien.