In search of safe and effective therapeutic agents as alternative to synthetic chemotherapeutics for the treatment of leukemia, the herbal drugs (Leaf of Madhuca longifolia, leaf of Prosopis cineraria and bark of Flacourtia indica) with long traditional use in West Bengal have received our attention. Present work was conducted to isolate and identify the active compounds of the selected herbal drugs using bio-assay guided fractionation and also to investigate their anticancer mechanism in leukemia cell lines. Bio-assay guided fractionation was used for the isolation of active constituents such as myricitrin, vitexin and vanillin from the aqueous extracts of M. longifolia, P. cineraria and F. indica, respectively using liquid partitioning and column chromatography and the compounds were characterized by HPLC, MS and NMR. Dose and time-dependent cytotoxicity of isolated compounds were studied against leukemia cells and their anticancer mechanism such as cell wall damage, nuclear damage, ROS and NO generation, SOD level, LDH release and lipid peroxidation were investigated. Aqueous extract of M. longifolia, P. cineraria and F. indica exhibited maximum anti-proliferative activity against HL-60 (Acute myeloid leukemia, AML, 72.06%), K-562 (Chronic myeloid leukemia, CML, 42.14%) and Jurkat (Acute lymphoblastic leukemia, ALL, 51.71%) cells. Myricitrin, vitexin and vanillin exhibited dose-dependent (IC-50 values 164.4, 147 & 29.22μg/ml) and time-dependent activity with maximum cytotoxicity at 48h. All these three compounds caused apoptosis in leukemia cells by inducing free radicals such as ROS (1.33-2.65 Arbitrary units) and NO (11.17-18.53μM), cell membrane damage and nuclear condensation which were evidenced by increased release of LDH (1326-1439 U/L), improved lipid peroxidation (10.19-14.41nM/mg protein) and reduced SOD level (6.2-9.21 U/mg protein) in leukemia cells. Based on anti-proliferative activity, the isolated phyto-compounds myrcitrin, vitexin and vanillin from M. longifolia, P. cineraria and F. indica could be developed as natural drugs for treating AML, CML and ALL leukemia types, respectively.