The aim of this study was the developing of biorefinery using zygomycetes fungus Mucor indicus and green microalga Chlorella vulgaris . The potential of M. indicus was investigated in the second generation biorefinery using corn stover as lignocellulose substrate, while C. vulgaris was survived in the third generation biorefinery. In the second generation biorefinery, the carbohydrate contents of corn stover were converted to fuels and valuable chemicals using an integrated process including dilute acid and enzymatic hydrolysis. First, to obtain the maximum recovery of carbohydrates containing in corn stover, the optimization of dilute-acid hydrolysis was performed by a response surface design. Under the optimal reaction conditions (i.e., 1.8 % v/v H2SO4, 121 ?C for 22 min), the hydrolysis resulted in the production of 270 g glucose per kg of dry corn stover (57.8 % theoretical yield) and 100 g xylose per kg of dry corn stover (84.0 % theoretical yield). The process was followed by applying enzymatic hydrolysis to dilute acid pretreated corn stover using cellulase. The glucose rich solution obtained from enzymatic hydrolysis was fermented by M. indicus anaerobically to produce ethanol (0.38 g per g consumed glucose). Then, M. indicus cells were separated, washed and re-fermented aerobically using dilute acid hydrolysis of corn stover. This stage was performed to produce ethanol in addition to increasing valuable fungal biomass containing lipid and valuable biopolymer, chitosan. The effects of addition of different nutrient sources, including fungal extract and yeast extract along with mineral salts, were also investigated to maximize lipid yield in M. indicus cells. Eventually, lipid and chitosan containing in fungal cell walls were extracted. Extracted lipid was converted into biodiesel and finally de-fatted cells were digested anaerobically to produce biogas. Overall, in the developing of second generation biorefinery using M. indicus , 72.2 mg chitosan, 21.4 g ethanol, 1.4 g biodiesel, 6.2 g animal feed, and 2.7 mL methane were produced per 100 g dry corn stover. In the developing of third generation biorefinery using C. vulgaris , first, the growth condition of microalgal cells such as heterotrophic, autotrophic, and mixotrophic regime were studied. The potential of enzymatic and dilute acid hydrolysate of corn stover obtained from second generation biorefinery were investigated as carbon source for heterotrophic and mixotrophic growth conditions. The mixotrophic conditions resulted in the maximum growth rate, lipid, and carbohydrate content in the cells and minimum proteins synthesis. Then the fractionation of valuable products such as proteins, carbohydrates, and lipids were performed using a combined bead milling and enzymatic hydrolysis .The cells were treated by bead milling and then hydrolyzed by different hydrolytic enzymes, including lipase, phospholipase, protease, and cellulase. The potential of individual enzymes as well as their mixture were investigated for the fractionation. The maximum yields of recovery for all components were obtained after enzymatic hydrolysis by lipase at 37°C and pH 7.4 for 24 h. The combination of bead milling and hydrolysis with lipase resulted in 88% lipid recovery in solid phase, while 74 % carbohydrate and 68 % protein were separated in the liquid phase. Also, the fermentation of microalgal cells after protein and lipid extraction and anaerobically digestion of their residue were investigated. Based on this process, 7.8 g protein, 22.4 g lipid, 6.8 g ethanol, and 2.4 mL methane were produced per 100 g dry C. vulgaris biomass. Comparison between second and third generation biorefinery showed that the developing of second generation biorefinery using corn stover and M. indicus has potential to exploit maximum 136 € per 1000 Kg dry corn stover, while the developing of third generation biorefinery using C. vulgaris suggest 2.5 times more economic benefits (331 € per 1000 Kg dry microalgal biomass)