Five mesophilic full-scale anaerobic digesters treating food waste (FW-digester), animal waste (AW-digester), and co-substrate of food waste and animal waste (CO-digesters) were monitored identify bacterial and archaeal communities and to quantify the effect of substrate characteristics on them, and to identify 'core' microorganism. The substrate characteristics and microbial communities of the FW-digester, AW-digester, and CO-digesters were statistically different. Organic concentration and [Na+] were identified as major variations that effect microbial community. Methanogen community was more diverse in AW-digester than in FW-digester. Methanogen community in CO-digester was as diverse as in AW-digester, and the most dominant species was Methanoculleus bourgensis same as in FW-digester. Twenty-one bacterial genera and four methanogen species were found in all digesters as a consequence of their metabolic versatility to degrade organic and inhibitor compounds. The results implied that these core microorganisms may contribute to maintaining a stable microbial ecosystem.