Lipid production in terms of oil percentage and fatty acid composition of Anabaena torulosa which was identified morphologically and genetically was studied  to determine its ability for biodiesel production, in response to salinity, nitrogen and phosphorus starvation stress; salinity ranging from 50 to 250mM NaCl, nitrogen and phosphorus regime (50%, NO₃-N , 50% PO₄-P of BG11 media). The results indicated that there was change in physiological behavior under these different stresses and illustration of these differences genetically. The results of oil analysis revealed that the lipid production increased when nitrogen and phosphorus decrease (68.83% and 160.97% respectively) and 200mM of NaCl increase oil content by 120%. GC/MS analysis of fatty acid composition revealed that methyl linoleate is the main constituent of fatty acids ester 57.9% which classified as a biodiesel due to its long methyl ester chain and is also used as a fuel in standard diesel engines. All these results explained genetically by using RAPD technique which revealed new bands appeared and other bands disappeared. DNA sequence was changed leading to DNA polymorphism 41.25%.  Also, the DNA pattern indicated that stress of nitrogen and phosphorus were more related to control, while the other stresses (salinity and combined stresses) caused more changes comparing to control. So that stress changes in physiology was confirmed genetically.