AIMS: To assess the impact of Bacillus amyloliquefaciens and Microbacterium oleovorans on bacterial and fungal groups associated to the roots of field-grown maize. METHODS AND RESULTS: Identification and count of bacterial and fungal culturable populations associated to the roots of maize seedlings, changes in culturable community structure according to the richness and diversity indexes concept and shifts in microbial activity through analysis of cellulolytic, ammonification and nitrification potentials were determined, in relation to kernel treatment with biological control agents. Following the treatment of maize kernels with B. amyloliquefaciens at 10(7) CFU ml(-1), an increase in bacterial diversity was observed at the rhizoplane of resultant seedlings. Bacterial richness was significantly increased at the root inner tissues of seedlings treated with Mic. oleovorans. Fusarium, Aspergillus, Penicillium and Trichoderma were the main fungal genera isolated and there population sizes were unequally affected by the addition of biocontrol agents. CONCLUSIONS: Numbers and types of isolated bacteria and fungi changed in response to the addition of biocontrol agents, while microbial activity remained unchanged with respect to control. SIGNIFICANCE AND IMPACT OF THE STUDY: This study provides an insight of the effects of proven biocontrol agents on micro-organisms naturally associated to the target crop.