Rapid development in nanotechnology and wide spread use of nano products increased probability of their release in aquatic and terrestrial ecosystems. Unique properties of nanomaterials and ambiguity in their transformation, reactivity and toxicity put a new challenge in front of scientists, government regulators and public stakeholders. In addition vital importance of soil microorganisms in soil as well as their diversity and lack of clear investigations about nanomaterial toxicity or other negative impacts on soil microorganisms show the necessity for more attention in this issue. Therefore the research community needs to focus on understanding the reactivity, mobility, fate, persistence and effects of nanomaterials in terrestrial ecosystems. This paper is trying to discuss some negative impacts of synthetic nanomaterials on soil microorganisms.