Fossil fuels are source of non-renewable energy and also have seriously negative impacts on the environment, e.g. soil, water, air, and climates. These problems are caused to serious attention in use of renewable energy resources by many countries. Regarding this matter, using the energy from biomass sources such as biogas and biohydrogen is one of the best options. Annual production of 33 million tones cotton in the world (in 2012) is associated with production of huge amounts of cotton plant wastes. In current study, potential of biogas and biohydrogen production from cotton plant wastes (cotton stalk and boll) was investigated. In order to improve yield of biogas and biohydrogen production, alkaline pretreatment was performed with 8% sodium hydroxide solution (by weight) at 0°C and 100°C for 10, 30 and 60 minutes, and with 4 and 8% ammonia solution (by weight) at 40°C and 80°C for 6 and 12 hours. Anaerobic digestion process was performed with mixed culture obtained from Isfahan North Wastewater Treatment sludge at mesophilic conditions at 37°C. Prior to biohydrogen production experiments, mixed culture was thermally pretreated at 85°C for 45 minutes to remove hydrogen consuming bacteria. According to the results, 80.8 and 88.5 mL CH 4 /g-VS was produced from untreated cotton stalk and boll, respectively. More biogas was produced from pretreated samples (except for the boll pretreated by 8% wt sodium hydroxide at 0°C for 60 min and the boll pretreated by 8% wt ammonia at 40°C for 6 h) compared to untreated ones. The maximal biogas production of 246.4 mL CH 4 /g-VS (78.3% of the theoretical value of methane production) was achieved from the boll pretreated by 8% wt sodium hydroxide solution at 100°C for 10 min. Furthermore, this pretreatment method led to the highest reduction in lignin content (31%) and the highest increase in glucan content (21.7%). Prolongation of sodium hydroxide at both temperatures (0 and 100°C) resulted in reduction of methane production; while more increment in methane production was achieved by performing the pretreatment at higher temperature compared to lower temperature. In addition, the best result by ammonia pretreatment of boll was obtained at the pretreatment condition of 4% wt ammonia concentration and 80 °C for 12 h. Increasing the temperature of ammonia pretreatment of boll at both ammonia concentrations (4 and 8% wt) resulted in more methane production. The highest methane production of 219 mL CH 4 /g-VS (76.6% of the theoretical value of methane production) was obtained from cotton stalk by 4% wt ammonia solution treatment at 80°C for 12 hours; whereas performing the pretreatment at lower temperature produced methane with lower yield. In addition, the best result by sodium hydroxide pretreatment of cotton stalk (205.4 mL CH 4 /g-VS) was obtained at the pretreatment condition of 8% wt sodium hydroxide concentration and 0°C for 60 min; while lower methane was produced from sodium hydroxide pretreated cotton stalk at higher temperature. . Amount of methane in produced biogas from pretreated materials was 54-61% in term of volume. Samples accompanied with the highest methane production, were used to hydrogen production. Once again, sodium hydroxide pretreated boll at the same conditions which led to maximum methane production, caused the maximal hydrogen production of 17 mL per gram of volatile solids. The highest hydrogen production of 15.2 mL per gram of volatile solids was achieved by 4% wt ammonia solution treatment. The results of the hydrogen production in this study showed satisfactory agreement with Gompertz equation, which is a kinetic model for describing substrate decomposition and biohydrogen production by batch method relative to the time. Crystallinity index measured by FTIR method for the untreated and treated cotton stalk by 8% wt sodium hydroxide and 4% wt ammonia were 0.85, 0.82 and 0.8, respectively; while these values for boll were 0.96, 0.74 and 0.78, respectively. SEM images of samples showed that the pretreated samples external surface area and their porosity were increased by pretreatment. Key words :Alkali pretreatment,Biogas,Biohydrogen, Cotton waste, Lignocellulosic materials.