Liquid-liquid extraction (LLE) techniques are widely used in separation primarily due to ease of scale up. Conventional (LLE) systems based on organic solvents are not suitable for extraction of fragile molecules such as proteins as it would result in denaturation. On the other hand aqueous biphasic system though suitable for extraction of proteins they are restricted by limited polarity range. Ionic liquids are salts which are liquid at room temperature. Ionic liquids have gained interest in extraction over the past years due to its non-volatility and tunable property. In this thesis we explored the feasibility of using two ionic liquid based systems for extraction: 1) Ionic liquid based aqueous two phase system for extraction of microalgae proteins and 2) ionic liquid based emulsions for separation of hydrophilic (e.g. proteins) and hydrophobic (e.g. pigments) components from complex biomass such as microalgae. Additionally the influence of IL pre-treatment on microalgae cell walls and subsequent fractionation of its components (e.g. proteins, pigments, lipids) was also investigated.