Quinone profiles and physico-chemical properties were measured to characterize the microbial community structure during a 14-day thermophilic composting of cattle manure mixed with rice straw as a bulking agent. The change in total quinone content (TQ) and the divergence of quinone (DQ) indicated that the microbial biomass reached a peak followed by a decrease, whereas the microbial community diversity increased continuously during the composting process. The high mole fraction of ubiquinones in the raw materials, and at the beginning of the composting period suggested that fungi and/or Proteobacteria were present. The predominance of MK-7 from days 3 to 7 suggested that Bacillus spp. were the main microbial species. An increase in partially saturated and long-chain menaquinones during the latter composting period indicated that the proliferation of various species of Actinobacteria was occurring. The microbial community structure, as expressed by TQ and DQ, corresponded well to physico-chemical properties such as the C/N ratio, pH, O-2 consumption and compost mass reduction. (C) 2003 Elsevier Ltd. All rights reserved.