Filamentous fungi produce a mixture of various metabolites such as pigments, fatty acids, proteins and other cellular metabolites. Thus, extraction and isolation of the pigmented molecules of interest are necessary steps before proceeding to any further utilization of these metabolites for commercial applications. Pigments can be stored within the biomass, excreted in the fermentation broth or both, suggesting that extraction methods need to be developed accordingly to the cellular localisation of the pigments and to their chemical natures. Despite the wide range of separation techniques currently available, most of industrial extraction processes rely on conventional liquid-liquid systems using organic solvent (hexane, dichloromethane, toluene, THF, etc.). Since environmental pollution generated by chemical industries has become a central concern in societal and political decisions, there is a growing demand for the development of efficient and greener separation technologies. Over the last two decades, and with the emergence of the concept of green chemistry, tremendous progresses have been performed in extraction and separation technologies. Methods such as ultra-sound-assisted extraction, microwave-assisted extraction, pressurised fluid extraction, supercritical fluid extraction, enzyme-assisted extraction, and more recently, ionic liquid assisted extraction were developed. The trend is to create extraction techniques involving cheap and environmental-friendly solvents that can be used under milder conditions with good final efficiency in quicker processes (ideally automatized). From the newest systems, ionic liquids have been recognized as very promising new extraction solvents due to the possibility to tailor their chemical properties and affinities to the target biomolecules. The focus of this work is to present an overview of the potentialities of the main emerging extraction methods on fungal matrixes for pigments isolation and recovery, with a particular interest for ionic liquids. Emerging greener extraction systems for fungal pigments isolation. Lebeau J.L.D., Venkatachalam M., Fouillaud M., Dufossé L., Caro Y.. Proceedings of the 8th International Congress of Pigments in Food – “Coloured foods for health benefits”, Cluj-Napoca, Romania, June 28 - July 01, 2016. Socaciu C. & Pintea A. (Eds.), University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Romania (Publ.), ISBN 978-606-8778-11-2, p 64, 2016.