Cyanobacterial lipids are considered as the feedstock of future sustainable biodiesel production, and extremophiles are usually preferred for biotechnological purposes to ease the cultivation problems. This study examines the total lipids and fatty acid composition of five novel cyanobacterial species isolated from extreme environments in the Almaty and Aktau regions: one unicellular Synechococcus and one filamentous Nostoc from Mangystau radon springs and two filamentous Oscillatoria, Phormidium elected from Chundzha thermal springs, as well as one filamentous Trichormus species collected from the salt lake Tuzkol, Kazakhstan. The lipid content of the isolated strains of cyanobacteria ranged from 14.2% to 22.1% of the cell dry weight, with the highest content observed in strains Oscillatoria subbrevis CZS 2201, Trichomus variabilis BK-1 and Nostoc calcicola ARS 2411 at 22.1%, 18.2% and 16.9%, respectively. In all studied cyanobacterial species’ cells, the main fatty acid was palmitic acid (16:0), followed by oleic acid (18:1n9) and minimal quantities of α-linolenic acid (18:3n-3) and long chain fatty acids (>C18). These strains produce fatty acids that improve oxidative stability and cold flow properties, with their balanced lipid profiles, including significant proportions of saturated and polyunsaturated fatty acids, further enhancing biodiesel quality.