Droplet digital PCR (ddPCR) is a new DNA quantification platform without an external DNA calibrator. This study examined methanogen communities in four full-scale anaerobic digesters treating municipal sewage sludge, using ddPCR with taxon-specific primer/TaqMan probe sets (5 orders, 11 families, and 13 genera), many of which were developed in this study. Total methanogen abundance was positively correlated with hydraulic retention time (HRT) and temperature (p < 0.05), though the effect of HRT was stronger (r = 0.864 vs. 0.682, respectively). Moreover, total abundance was strongly correlated with biogas production rate (r = 0.896). HRT was positively correlated with seven methanogenic taxa, while temperature was positively or negatively correlated with 13 taxa (p < 0.05). For instance, the predominant genera Methanosaeta and Methanosarcina were negatively and positively associated, respectively, with temperature only (p < 0.05). Redundancy analysis and principal component analysis using the absolute-abundance dataset indicated that only temperature explained the variability in the methanogen communities at all classification levels. Therefore, HRT was the most important operational factor to influence net methanogen abundance and activity, while temperature governed the composition of the methanogen community. ddPCR enabled absolute quantification of methanogens without the external DNA standards and linked methanogen communities and operational factors, suggesting that it is a promising tool for analyzing the microbial ecology of anaerobic digestion.