Aim: To investigate the impact of inoculating peanut seeds with the biocontrol agent Trichoderma harzianum ITEM 3636 on the structure of bacterial and fungal communities from agricultural soils. Methods and Results: Polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (PCR-DGGE) and next-generation sequencing (NGS) of amplicons (or marker gene amplification metagenomics) were performed to investigate potential changes in the structure of microbial communities from fields located in a peanut-producing area in the province of C ordoba, Argentina. Fields had history of peanut smut (caused by Thecaphora frezii) incidence. The Shannon indexes (H 0 ), which estimate diversity, obtained from the PCR-DGGE assays did not show significant differences neither for bacterial nor for fungal communities between control and inoculation treatments. On the other hand, the number of operational taxonomic units obtained after NGS was similar between all the analysed samples. Moreover, results of alpha and beta diversity showed that there were no significant variations between the relative abundances of the most representative bacterial and fungal phyla and genera, in both fields. Conclusions: Trichoderma harzianum ITEM 3636 decreases the incidence and severity of agriculturally relevant diseases without causing significant changes in the microbial communities of agricultural soils. Significance and Impact of the Study: Our investigations provide information on the structure of bacterial and fungal communities in peanut-producing fields after inoculation of seeds with a biocontrol agent. peanuts, although its production represents <2% of the world's production (Pedelini 2014). Peanut plants are susceptible to a large number of diseases that develop due to numerous factors such as the susceptibility of the cultivar to diseases, type of pathogen (fungi, bacteria or viruses), a favourable environment and biotic factors (including the microbiota associated to the plant). Such factors are part of the tetrahedron of the disease described by Brader et al. (2017). Within a favourable environment, Journal of Applied Microbiology 126, 608--623