Among the products of pyrolysis is an aqueous phase (AP), which contains a significant fraction of carbon but is too dilute to make recovery of this organic content cost-effectively. This study was to explore the use of AP for anaerobic digestion. Different treatment methods including overliming, Fenton's reagent oxidation, bleaching and activated carbon adsorption were investigated to reduce toxicity of AP. Overliming treatment increased biogas production up to 32-fold compared to non-treated AP. Enhancing the tolerance of the bacterial and archaeal community to the AP toxicity was also attempted with a directed evolution method, resulting the microbes' tolerance to AP from 5% to 14%. Directed evolution resulted a major bacterial taxa as Cloacimonetes, Firmicutes, and Chloroflexi, while shifted the predominant archaea shifted from acetoclastic to hydrogenotrophic methanogens. Collectively, the results demonstrated that combining feedstock treatment and directed evolution of the microbial community is an effective way for AP anaerobic digestion.