Nannochloropsis sp. has been a very attractive microalgae species because of its high omega-3 fatty acid content. However, it is also one of the species with the strongest cell wall. Currently, energy-intensive mechanical techniques and harmful and flammable organic solvents are used for extracting lipids from Nannochloropsis sp. biomass. Thus, in this study, cholinium [Ch] amino acid-based ionic liquids (ILs) were investigated for their capability to extract lipids from Nannochloropsis sp. Among all the ILs tested, cholinium arginate ([Ch][Arg]) extracted the highest amount leaving only 1.4 +/- 0.2% lipid in the remaining biomass. The extraction was still efficient at room temperature leaving only 7.9 +/- 0.3% lipid. Thus, [Ch][Arg] is an efficient green solvent for Nannochloropsis lipid extraction.