In this study, the increase in lipid content of Chlorella emersonii and Chlamydomonas starrii microalgae and biofuel production in biorefinery were investigated. Green microalgae Chlorella emersonii and Chlamydomonas starrii were used in this study due to their ability to grow in different conditions and produce a significant percentage of lipids and carbohydrates. The phototrophic culture was investigated in three light intensities of 40, 95, and 140 ?mol m-2 s-1 and bicarbonate reception at different concentrations of 0.5 to 4 g.l-1 sodium bicarbonate. At a light intensity of 40 ?mol m-2 s-1, the maximum biomass concentration and biomass productivity were obtained 0.09 g.l-1 and 0.007 g.l-1.day-1, respectively. The optimum concentration for culture with sodium bicarbonate was 2 g/l, which the maximum biomass concentration and biomass productivity were obtained 0.5 g.l-1 and 0.019 g.l-1.day-1, respectively. Photoheterotrophic cultures were also studied at different concentrations of 1, 2, and 4 g.l-1 glucose. The maximum biomass concentration and biomass productivity of this condition were obtained 0.4 g.l-1 ,and 0.067 g.l-1.day-1, respectively. The lipid content of these two species was studied as a two-stage culture under different stresses of nitrogen and phosphorus deficiency, high light (357 ?mol m-2 s-1), high salinity (150 mM sodium chloride), and 3-fold nitrogen concentration. The best stresses for Chlorella emersonii and Chlamydomonas starrii were salinity and phosphorus deficiency, respectively. The lipid content of Chlorella emersonii microalga was enhanced by 33% under high salinity stress and by 18% for Chlamydomonas starrii microalga under phosphorus stress. After preparing the biomass required for the study, lipid was extracted and converted to biodiesel through in situ transesterification, and 420 and 299 mg of biodiesel per gram biomass were obtained from the microalgae lipids of Chlorella emersonii and Chlamydomonas starrii, respectively. The residual biomass from lipid extraction was first subjected to enzymatic hydrolysis, and the hydrolysis efficiencies for Chlorella emersonii and Chlamydomonas starrii were calculated to be 22.95 and 20%, respectively. Then, by separate fermentation of glucose released in saccharomyces cerevisiae, 0.44 and 0.43 g of ethanol per gram of fermentable glucose were obtained. Keywords: Photoautotrophic, Biodiesel, Chlorella emersonii, Chlamydomonas starii, two-stage cultivation, Bioethanol