Microbial population dynamics were evaluated in anaerobic codigesters treating municipal solid waste and sewage sludge. Ribosomal RNA based oligonucleotide probes were used to characterize changes in population abundance of syntrophic volatile fatty acid degrading bacteria and methanogens. Changes in community structure were linked to traditional performance parameters during the recovery of previously unstable codigesters induced by a reduction in mixing levels. Methanosarcina spp. were the most abundant aceticlastic methanogens in unstable codigesters with high acetate concentrations, while Methanosaeta concilii was dominant in stable systems with low levels of acetate. Growth of Syntrophobacter wolinii was enhanced during stabilization of a codigester with a well-developed population of Methanobacteriaceae, possibly because the presence of adequate numbers of these hydrogenotrophic methanogens encouraged the syntrophic oxidation of propionate. Mesophilic saturated fatty acid beta-oxidizing syntrophs were most abundant in previously unstable codigesters. One minimally mixed reactor became unstable after switching to continuously mixed conditions. After the switch, total archaeal abundance decreased sharply, though Methanobacteriaceae and Methanosarcina spp. levels increased as the fermentation became unbalanced. Based on the results presented here, mixing appears to inhibit the syntrophic oxidation of volatile fatty acids, possibly by disrupting the spatial juxtaposition of syntrophic bacteria and their methanogenic partners.