This review addresses the possible ecological effects of transgenic plants on micro-organisms in the field, hence, in the phytosphere and in the soil matrix. The important steps involved in the interaction between plant DNA and bacteria and the factors that influence the horizontal gene transfer (HGT) process will be discussed. HGT is a process in which two partners are involved, even if indirectly. In the first section, aspects concerning bacteria, such as their physico-chemical, biological and genetic characteristics, are described. Parameters affecting transgenic DNA fate in the environment are described in the second section. Subsequently, terrestrial habitats are evaluated in terms of their capacity to favor horizontal gene transfer. Finally, we focused on several studies in order to evaluate possible perturbations of soil bacterial community composition due to cultivation of transgenic plants in the field.