An aqueous two-phase system (ATPS) was employed as the solvent in extraction and enrichment of genistein and apigenin from pigeon pea roots. The partition behaviors of target compounds were investigate first. ATPS with 28% ethanol and 22% K2HPO4 was chosen for the extraction and enrichment of genistein and apigenin, the recoveries were 93.8% and 94%, respectively. The optimized conditions under microwave-assisted with ATPS were power 300W. liquid/solid ratio 30:1, temperature 50 degrees C and time 10 min. The extraction yields of genistein and apigenin were 0.439 +/- 0.198 mg/g and 0.207 +/- 0.113 mg/g, meanwhile the purity of genistein and apigenin reached 0.471% and 0.233% with an increase of 110% and 85% to those extracted by 80% ethanol. Furthermore, the antioxidant activities of extracts with ATPS were 2.673 mmol FeSO4/g DW and IC50 value 0.108 mg/ml by the FRAP assay and DPPH assay. (C) 2012 Elsevier B.V. All rights reserved.