We Determined the Effect of Different Mixing Intensities on the Performance, Methanogenic Population Dynamics, and Juxtaposition of Syntrophic Microbes in Anaerobic Digesters Treating Cow Manure from a Dairy Farm. Computer Automated Radioactive Particle Tracking in Conjunction with Computational Fluid Dynamics Was Performed to Quantify the Shear Levels Locally. Four Continuously Stirred Anaerobic Digesters Were Operated at Different Mixing Intensities of 1,500, 500, 250, and 50 Revolutions Per Min (RPM) over a 260-Day Period at a Temperature of 34 ± 1°C. Animal Manure at a Volatile Solids (VS) Concentration of 50 G/L Was Fed into the Digesters Daily at Five Different Organic Loading Rates between 0.6 and 3.5 G vs./L Day. the Different Mixing Intensities Had No Effect on the Biogas Production Rates and Yields at Steady-State Conditions. a Methane Yield of 0.241 ± 0.007 L CH 4/g vs. Fed Was Obtained by Pooling the Data of All Four Digesters during Steady-State Periods. However, Digester Performance Was Affected Negatively by Mixing Intensity during Startup of the Digesters, with Lower Biogas Production Rates and Higher Volatile Fatty Acids Concentrations Observed for the 1,500-RPM Digester. Despite Similar Methane Production Yields and Rates, the Acetoclastic Methanogenic Populations Were Different for the High- and Low-Intensity Mixed Digesters with Methanosarcina Spp. and Methanosaeta Concilii as the Predominant Methanogens, Respectively. for All Four Digesters, Epifluorescence Microscopy Revealed Decreasing Microbial Floc Sizes Beginning at Week 4 and Continuing through Week 26 after Which No Microbial Flocs Remained. This Decrease in Size, and Subsequent Loss of Microbial Flocs Did Not, However, Produce Any Long-Term Upsets in Digester Performance. © 2007 Wiley Periodicals, Inc.