In this work, different ionic liquids composed by choline as cation and amino acid as anion (CAAILs) have been synthetized and applied to establish aqueous two-phase systems (ATPS) with two phosphate salts. In order to understand the phase formation process of the ATPS, binodal curves, tie-lines and their respective tie-line lengths were determined at T = 298.15 K and atmospheric pressure. Besides, the tie-lines were fitted using Othmer-Tobias and Bancroft equations. Furthermore, with the aim to analyse the application of the studied ATPS in the recovery of flavonoids, partition coefficients of rutin and quercetin were calculated at T = 298.15 K and atmospheric pressure. Finally, the obtained results were compared with those found in literature. (C) 2019 Elsevier B.V. All rights reserved.