Two full-scale anaerobic digesters, one a clarigester purifying a maize processing wastewater and the other with an upflow anaerobic sludge blanket (UASB) configuration treating brewery effluent, contained well settling, granular sludges efficient in pollutant removal. Due to differences in both digester design and feed composition, the sludges differed in activity and microbial population. The clarigester granules contained a diverse population with a multiformity of hydrolytic, acidogenic and acetogenic bacteria while the predominant methanogens, in order of significance, were Methanothrix and Methanosarcina. These granules did not reconstitute on re-start up following digester shutdown and possible reasons for this are discussed. The UASB granules contained a more uniform population with three major microbial morphotypes, the predominant methanogens being Methanothrix and, possibly, Methanobacterium. In this paper the differences in digester design, feed composition, sludge microbiology and process performance are discussed.