Anaerobic digestion (AD) is a process of degradation of organic matter by microorganisms in an oxygen-free environment, which produces biogas, a vital renewable energy source. Using solely an organic source, such as monosubstrates, it is difficult to optimize the AD process due to nutrient imbalance, lack of appropriate microbial communities, and the effect of operational parameters. This chapter reviews the current studies on biogas production from the anaerobic codigestion process of mixing agricultural byproducts, focusing on rice straw and livestock manure as substrates. Because rice straw is high in cellulose, it needs to be pretreated before feeding into the anaerobic digester. Different rice straw pretreatments are summarized including physical, chemical, and biological methods. Current biogas systems are discussed. The utilization of bioslurry from the anaerobic fermentation process to agricultural cultivation and aquaculture activities is also discussed.