<P><B>Abstract</B></P> <P>Dynamic changes in microbial communities and digestion performance of AFEX treated corn stover co-digestion were compared to untreated corn stover co-digestion. Even though it took longer to stabilize the AFEX treated corn stover co-digestion system than it did for the untreated corn stover co-digestion, the results show that AFEX treated corn stover is a good feedstock to enhance the <I>archaea</I> community and improve biogas production. In the stabilized digestion system, the AFEX treated corn stover co-digestion increased abundance of archaea community (11.8%) by approximately three times compared to the untreated corn stover co-digestion (4.3%), The corresponding biogas production (213 L/kg VS loading) of the AFEX treated corn stover co-digestion was 22% higher than that (175 L/kg VS loading) of the untreated corn stover co-digestion. AFEX treatment could enable more extensive use of lignocellulosic biomass for anaerobic digestion to generate biogas and thereby provide another route for lignocellulosic biofuel production.</P> <P><B>Highlights</B></P> <P> <UL> <LI> AFEX treated corn stover enhanced biogas production of anaerobic co-digestion. </LI> <LI> Microbial communities were significantly shifted by co-feeding AFEX treated corn stover. </LI> <LI> Co-feeding AFEX treated corn stover is in favor of archaea accumulation in the digestion. </LI> <LI> With appropriate pretreatment lignocelluloses can be feedstocks for anaerobic digestion. </LI> </UL> </P>