The microbial community residing in digesters largely remains a black box [65]. This is largely attributed to the difficulties and inability to grow these microbes in laboratory media. The use of cultivation-independent DNA-based molecular biology and metagenomic techniques makes it possible to define the membership and functionality of this complex microbial community (e. g., reviewed in [41]). As indicated by the more than 5,265 bacterial and 839 archaeal 16S rRNA gene sequences of anaerobic digester origin archived in the Ribosomal Database Project (RDP) (as of this writing, unpublished data), our knowledge on this microbial community has expanded tremendously [61,65]. These sequences represent approx­imately 2,500 species of bacteria (based on 97% 16S rRNA gene sequence identity) and 160 species of archaea (unpublished data). Our statistical prediction suggests that AD reactors can have at least 3,500 species of bacteria and 170 species of archaea. The continued studies using both molecular biology and metagenomic techniques should provide a better knowledge on the microbial community struc­ture, population dynamics, adaptation, granulogenesis, and metabolic kinetics in digesters. Eventually, this knowledge will help develop more efficient and stable AD technologies.