Microbial-based indicators of soil quality are believed to be more dynamic than those based on physical and chemical properties. Recent developments in molecular biology based techniques have led to rapid and reliable tools to characterize microbial community structures. We determined the effects of conventional and no-tillage in cropping systems with and without cover crops on bacterial community structure, total organic carbon (TOC) and soil aggregation. Tillage and rotation did not affect TOC from bulk soil. However, TOC was greater in the largest aggregate size class (7.98-19 mm), and had greater mean-weight diameter under no-tillage than under conventional tillage in the 0-5 cm soil layer. Soil bacterial community structure, based on denaturing gradient gel electrophoresis of polymerase chain reaction amplified DNA (PCR/DGGE) using two different genes as biomarkers, 16S rRNA and rpoB genes, indicated different populations in response to cultivation, tillage and depth, but not due to cover cropping. Soil bacterial community structure and meanweight diameter of soil aggregates indicated alterations in soil conditions due to tillage system. © 2005 Elsevier B.V. All rights reserved.