Filamentous fungi have been widely recognized as promising sources of various types of biomolecules and are therefore highly investigated. The production of fungal pigments is one intensively studied domain in order to respond to the growing demand for natural colorants as substitutes to synthetic dyes used in food, cosmetics, pharmaceutical and textile industries. Such interest in the natural origins of the pigments is driving the search for new and greener extraction systems. It is desired to develop extraction processes that would use less organic solvents and milder conditions, allow higher and quicker extraction yields, as well as improved selectivity and better recovery. Over the last two decades, ionic liquids (ILs) have caught attention as novel green solvents, and have already been applied in various separation systems (membranes separation, additives in mobile phase and surface-bonded stationary phases in chromatography) [1]. ILs are molten salts that can display a vast variety of chemical properties based on the specific association of a bulky and asymmetric organic cation with an organic or inorganic anion. The use of an aqueous two-phase systems (ATPS) based on ionic liquids allows to tailor the extraction system to the pigmented molecule of interest, here fungal pigmented polyketides. In this study, several ATPS based on quaternary ammonium ([N4444]Br-) and immidazolium ([C4Mim]Cl- and [C4Mim]Br-) ionic liquids were investigated for the efficient extraction and recovery of soluble polyketides pigments from the fermented broth of four fungal strains: Talaromyces albobiverticillius, Emericella purpurea, Penicillium marquandii, Trichoderma harzianum. These four families are known to produce mainly polyketides pigments such as azaphilone and hydroxyanthraquinone pigments, which are the main targets in the field of fungal pigments research [2,3]. The extraction efficiency of red, orange and yellow hues was investigated with a particular focus on the soluble red pigments extraction efficiency and recovery from the three different ATPS tested. The results showed that extraction yields of extracellular pigments of all hues from all strains are greater than 80%, with [N4444]Br- and [C4Mim]Cl- reaching between 90 and 100% extraction efficiencies. Moreover, these two IL-based ATPS tend to preferably isolate red pigments under alkaline conditions, which is in agreement with previous studies [4]. The second step of this study, which focused on the recovery of the different pigments from the ILs, remains under investigation as the affinity of the IL for the pigmented molecules seems high and difficult to reverse. Nevertheless, the initial results of this study bring novel strategies for the selective extraction of extracellular fungal pigments. As a next step, further investigation would be required in determining the specific solubility of azaphilones and hydroxyanthraquinones-like molecules in the different ILs.