For the first time, different types of diethylaminoethyl (DEAE) anion-exchange resins, widely used in previous studies, were investigated to determine the most effective resin for the purification of microcystins (MCs). MCs were extracted from freeze-dried Microcystis aeruginosa cells that had been harvested from the Bueng Nong Khot reservoir, Khon Kaen, Thailand. The toxins were precipitated with ammonium sulfate and then fractionated using five different anion-exchange chromatography resins, followed by chromatography with a C18 cartridge. The toxins were further identified via liquid chromatography–electrospray ionization–mass spectrometry (LC-ESI-MS) analysis, and the yields and purity were determined by high-performance liquid chromatography (HPLC) with ultraviolet detection. DEAE Sephadex A-25 exhibited the best overall performance for MC purification regarding both yield and purity, followed by DEAE cellulose, DEAE Sephacel, DEAE Sepharose Fast Flow and Toyopearl DEAE. Four MC variants, MC-RR, MC-FR, [Dha7]MC-LR and MC-WR, were obtained, and [Dha7]MC-LR was the major variant, with a total yield of 53.08 mg and a purity of 95% using the Sephadex resin. This study indicates that protein precipitation and single-column chromatography using DEAE Sephadex A-25 constitute an effective method for the purification of a wide range of MC variants.