Anaerobic digestion (AD) is a biological conversion method that can make an important contribution to sustainable wastewater treatment as it stabilizes organic waste together with the simultaneous recovery of energy in the form of biogas. Since the emission of dangerous pollutants is low, the valorisation of the biogas produced (consisting of approximately 65% ​​CH4, 35% CO2 and trace gases such as H2S, H2 and N2) is energy efficient and ecological (Apples et al , 2011). With energy recovery from waste, AD has dramatically changed the concept of waste treatment from the perspective of pollution control to the recovery of valuable resources from waste (Carballa et al., 2011). In addition to energy recovery, AD has several other advantages, such as low sludge production, no need for aeration, low nutrient requirements, etc., which make AD a preferred option for treating high resistance wastewater. AD has been widely used for wastewater treatment purposes, especially since the introduction of the Upflow Anaerobic Sludge Blanket (UASB) reactor approximately 25 years ago. High solids retention time (SRT) is achieved by self-immobilization of microbial communities in granulated form, which is preserved longer in anaerobic reactors. Although various other types of anaerobic bioreactor designs have been developed (e.g., expanded granular sludge blanket, internal circulation reactors, etc.), UASB reactors are still the most common and preferred choice worldwide (Franklin 2001) . Although both reactor engineering and process design approaches for wastewater treatment plants have grown, a huge discrepancy exists between the knowledge developed by engineers and the understanding of the microbial ecology of AD. And this gap is the reason behind the instability problem in AD there... half of the article... the review is dedicated to improving the AD process in view of a shift in focus from sophisticated reactor engineering to microbial community structure engineering. Since the molecular methods available to study microbial community structure have been well reviewed (Rastogi and Sani, 2011; Talbot et al., 2008; Vanwonterghem et al., 2014), only a brief description of several culture-independent techniques applied in Anaerobic wastewater treatment systems are provided in Section 2. Section 3 will highlight how the microbial community structure has been studied under different process conditions to reveal the “black box” of anaerobic digestion. In Section 4, a perspective on emerging modeling approaches with the inclusion of microbial data is offered. Alongside Section 4, a critical discussion highlighting current gaps and most important areas in future AD research is provided.