ABSTRACT Microorganisms are excellent soil quality indicators because their properties within the soil community change quickly in response to changes in the surrounding environment. The aim of this study was to determine if the structure and diversity of soil bacterial and fungal communities were useful for discriminating cut flower cultures under conventional (CM), ecological (EM), and intermediate (IM) management practices. Results obtained by PCR-DGGE revealed that bacteria had lower similarity in structure and higher diversity under EM than under CM. Sites under IM showed greater similarities in structure and diversity to the site under CM, although there were still significant differences between them. Fungal structure showed higher similarity among sites, with differences in diversity only between EM and CM. In the sites studied, bacteria, rather than fungi, were good indicators of changes in soil quality. The results of this study confirmed that EM and IM promote soil bacteria diversity.