Scarce information is available on the changes in abundance of microbial taxa during vermicomposting. Quantitative PCR and DGGE analysis were used to monitor variations in the microbial structure, relative abundance of four bacterial classes and fungi over the vermicomposting and maturation period of wet olive cake (O) and vine shoots (W). Multivariate correlation analysis between microbial structure and abundance, earthworm biomass and enzyme activities revealed similar and divergent interactions in both processes. Although Eisenia fetida development was different, significant correlations were found with beta-glucosidase activity and with bacterial and fungal structure. In the vermicomposting period of O and W, a decline was found in bacteria (94% and 77%), fungi (93% and 94%), and Gammaproteobacteria (56% and 71%) but an increase in Betaproteobacteria and Actinobacteria (62-79%). Alphaproteobacteria increased only in O (26%). Despite the different initial lignocellulose wastes, the mature vermicomposts were similar in microbial and biochemical properties. (c) 2013 Elsevier Ltd. All rights reserved.