Two laboratory-scale systems were set up (i) composting (without earthworms) and (ii) vermicomposting (with earthworms) and were monitored for 60 days after pre-composting. The physico-chemical parameters (pH, C/N, organic matter, NH(4)(+)-N and ash content) showed similar evolution in both systems except a higher NH(4)(+)-N in the initial vermicomposts. However, principle component analysis (PCA) of enzymatic activities and community level physiological profiles revealed differences in the functional response of microbial communities in compost and vermicompost during maturation. Dehydrogenase activity and bacterial counts indicated a steady decrease in biological activity and population during composting, whereas vermicomposting exhibited higher activity on day 30 and a reduction in bacterial counts on day 10. PCA of denatured gradient gel electrophoresis (DGGE) profiles showed divergent dynamics of bacterial communities in two processes. These results indicated differences in the functional response and genetic structure of microbial community in composts and vermicomposts despite similar changes in their physico-chemical parameters.