In the traditional Indian medicine, the roots and leaves of Cissampelos pareira are administered for the relief of diarrhoea and antiseptic against inflammation. The present investigation is to optimize the suitable extraction method and thereby isolating and characterizing various bioactive leads from the leaf and stem portion. Preliminary phytochemical screening reveals the presence of maximum alkaloids and moderate quantity of flavonoids and saponins with dichloromethane as solvent. In leaf portion, the hot extraction method was suited as the alkaloid content seems to be maximum, whereas in stem portion, the cold maceration was suited with more flavonoid content. This was evidenced further with higher yield values obtained for leaf extract (56% w/w) rather than stem extract (39.5% w/w). Two pure bioactive leads were isolated, each one from leaf (CP*) and stem (CP**). CP* of leaf (80% CHCl3-MeOH) was identified as alkaloid by qualitative analysis (Dragendroff's reagent); TLC analysis (Rf: 0.88, Toluene: EtoAc: GAA (7:2:1)); U.V analysis (lmax: 265nm, Chromophore: C=N; Transition: p-p* (forbidden)); I.R spectra (2919-2850 cm–1; 2346 cm–1; 1724 cm–1; 1166 cm–1; 720 cm–1) and Mass spectra (M-229) fragmentation peak for the presence of Bebecrine after elucidation. In addition CP** of stem (60% CHCl3–MeOH) was identified as isoquinoline alkaloid by qualitative analysis (Hager's reagent); TLC analysis (Rf : 0.95; Toluene: EtoAC: Diethylanine (7:2:1); U.V analysis (lmax: 265nm); I.R. spectra (3774–3378 cm–1; 2926–2974 cm–1; 23.47–2132 cm–1; 1927 cm–1; 1728–1665 cm–1; 1378–1256 cm–1; 1089–1049 cm–1; 880–758 cm–1); and Mass spectra (M+1 607) for the presence of cissampareine, which is reported for the first time from stem portion.