The addition of fresh organic matter is known to modify both microbial community structure and soil aggregation. The objective of this study was to understand the relationship between the dynamics of the soil microbial community structure in relation to that of their habitats during the decomposition of straw. Soil samples, ground (<200 mu m) to remove macroaggregates, were amended with uniformly C-13-labelled powdered rice straw (<500 mu m) and incubated for 21 days. Unamended control samples were also incubated under the same conditions. Total C and rice straw C (C-Straw) mineralised or remaining in different soil fractions (0-50, 50-200, 200-2000 and >2000 mu m) were measured. Fatty acid methyl ester (FAME) profiling was used to determine total bacterial community structure and FAME based stable isotope probing (FAME-SIP) was used to characterise the straw degrader communities. The mineralisation rate of the native C and the C-Straw was high. The formation of macroaggregates (>2000 mu m) occurred within 2 days in amended and unamended samples but did so to a greater extent in the amended samples. The C-Straw was mainly located in fractions >200 mu m, where degraders were the most abundant. The C-13-FAME profiles followed the same trends as total FAME profiles through time and within soil fractions, suggesting common dynamics between straw degraders and total bacterial communities: Gram-negative were more important in fraction >200 mu m and during the early stages of the incubation while Gram-positive and actinobacteria dominated in fine fractions and at the end of the incubation. Bacterial community structure changed rapidly (within 2 days) in conjunction with the formation of new microbial habitats, suggesting that the relationship between the two is very close.