One of the most crucial factors determining the safety and efficacy of any herbal medicine or natural product-based formulation is the quality of the raw material. The absence of readily available bio-markers (standards) is one of the hurdles which need to be overcome to develop robust and effective quality control protocols.Aloe ferox Mill. is a most coveted ethnomedicinally import plant indigenous to South Africa. A. ferox has been used since ancient times in folk medicine and recently it has gained popularity as an ingredient in cosmetic formulations and food supplements. This study aimed to develop a superior method for the isolation of bio-markers from “aloe bitters” (exudate) obtained from A. ferox.For separation by HPCCC the solvent system comprising of EtOAc/n-BuOH/H2O (3.5:1.5:5, v/v/v) was used in reversed phase mode. By this method, and only in one run, eight bio-markers were separated and isolated on semi-preparative scale including aloesin, aloeresin C, aloeresin A, 5-hydroxyaloin, aloin B, aloinoside B, aloin A and aloinoside A. The isolation of bio-active molecules from A. ferox (Cape aloes) is presented to illustrate the efficiency and advantages of high performance counter-current chromatography (HPCCC).