Phylogenetic analysis was performed based on ITS 1 and 2 sequences to determine monophyly of Datura and Brugmansia and to understand their relationships. The results support the splitting of Datura and Brugmansia into two distinct genera (BS 100 & 91). D. ceratocaula earlier considered as the connecting link between the two genera, is nested within the Datura clade (BS 57) as a distinct species. Although the three conventional sections of Datura viz. Dutra, Ceratocaulis & Datura (Stramonium) stand well supported (BS 100, 100 & 83), D. kymatocarpa, D. leichhardtii and D. pruinosa appear shifted from Section Dutra to Section Datura, corroborating earlier observations. D. discolor remains nested within the Section Dutra, refuting earlier suggestions as intermediary or ancestral role. But the divergence of D. discolor from the remaining taxa within the section Dutra as a clearly supported subclade (BS 100) may be suggestive of the subdivision of Section Dutra into two subsections. This subdivision of section Dutra however remains to be appraised using cladistical studies incorporating both molecular and morphological data. The infrageneric grouping of Brugmansia into cold and warm groups viz. sections Sphaecarpium and Brugmansia exclusively on the basis of fruit shape and habitat lacks adequate support in the present analysis. But fruit shape appears not consistent as the warm climatic inhabitant B. aurea with trumpet shaped flowers sports egg-shaped fruits. Hence we propose subdivision of the genus into two sections on the basis of the more stable corolline form, and the proposition is well supported by molecular data viz. section Brugmansia (with trumpet and/or funnel shaped flowers, with fruits fusiform or egg-shaped) and section Sanguinea (with tubular flowers and consistently egg-shaped or short oval fruits).