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ue to unsustainability of petro derived fuels, the world is now concerned about alternative, sustainable and eco-friendly energy production. As a successful alternative energy, biodiesel plays a major role to replace petrodiesel. Cyanobacterial lipids have great potential for biodiesel production due to their rapid growth rate and renewability. The production of biodiesel from biomasses depends on upstream (lipid extraction) and downstream (trans-esterification) processes. Lipid extraction should be effective and energy efficient to reduce the production cost of commercial biodiesel production. Therefore, the present study was experimented to optimise the lipid extraction solvent system from cyanobacteria. Cyanobacteria samples were collected from Beira Lake, Colombo where, Microcystis spp. are dominant (> 96 %). Solvent systems n-hexane, chloroform: methanol (2:1), n-hexane: ethanol (3:2), chloroform: n-hexane (1:1), dichloromethane: methanol (1:1), n-hexane: isopropanol (2:3) and diethyl ether were used for lipid extraction and subjected to optimisation for the lipid extraction method from the cyanobacterium Microcystis spp. Extracted lipid yield (g/1 g of dried biomass) for each solvent system was 1.11 wt. %, 1.61 wt. %, 1.71 wt. %, 2.15 wt. %, 3.41 wt. %, 4.33 wt. % and 1.95 wt. %, respectively where fatty acid methyl ester (FAME) compositions found to be 80.13 %, 78.27 %, 76.39 %, 29.01 %, 85.72 %, 92.39 % and 80.09 % in each system. The gas chromatographic-mass spectrometry analysis of the products revealed that the most abundant fatty acid types of Microcystis spp. were palmitic acid (C16:0) and its derivative such as 14-methyl pentadecanoic acid. The highest lipid yield (4.33 wt. %) and fatty acid methyl ester (92.39 %) composition were recorded from n-hexane: isopropanol solvent system.