Microbial biomass and community structure were investigated in two composts using the phospholipid fatty acid technique. The composts consisted of shredded straw of Miscanthus with the addition of pig slurry to give an initial C:N ratio of about 25. Samples were taken following changes in the compost temperature (at 5°C intervals) during the first month of composting and additionally after 2 and 3 months. The total microbial biomass, measured as total amount of phospholipid fatty acid, peaked after 1 day with about six times the initial values. The temperature also peaked after 1 day, being above 60°C, and then slowly declined to around 25°C over 3 months. Microbial biomass was approximately halved during this time. When the total amount of phospholipid fatty acid was separated into indicator phospholipid fatty acids for different groups of microorganisms, these groups showed different patterns during the composting process. Gram-positive bacteria increased rapidly with increasing temperature and decreased with decreasing temperature. Gram-negative bacteria and fungi increased initially up to a temperature around 50°C, but decreased during the extreme heating phase. When the temperature declined to about 50°C, the amounts of phospholipid fatty acids indicative of these two groups increased again. The phospholipid fatty acid indicative of actinomycetes, 10Me18:0, was at a low level during the whole experiment, but increased slightly during the last month of composting. The development of the microbial community in the two composting systems was similar during the initial thermophilic phase of the composting process, but the communities after 3 months differed.