The utilization of biodiesel is an alternative step to meet the energy needs of fossil fuels that will gradually decline. Supported by the potential of Indonesia's marine wealth, microalgae serve as a promising biodiesel raw material candidate. The purpose of this research is to understand the effect of physiological stress of N (nitrogen) and Si (silica) nutrients on growth and lipid content of microalgae Skeletonema costatum as biodiesel fuel candidate. The method used in this research was S. costatum culture in intermediate scale as much as 8 L. Making growth curve by counting cell density by using hemacytometer Harvesting was done at the end of the exponential phase. Then tested lipid content qualitatively with fluorescence microscope. The results obtained were the highest cell density on N3SÌ2 (KNO3 0 g / L and Na2SiC>315 g / L), while the N2SÌ3 treatment (KNO3 37.5 g / L and Na2SiC>3 0 g / L) was the lowest cell density. Accumulation of lipids in the treatment of N2SÌ2 (KNO3 37.5 g / L and N a 2 S i 0 3 1 5 g / L).