This special issue of ESPR is focused on microbial ecotoxicology. What is ‘microbial ecotoxicology'? It is a branch of science that studies both (i) the ecological impacts of chemical (synthetic or natural origin) or biological (toxic species) pollution at the microbial scale and on the various functions that they ensure in the ecosystems and (ii) the role of microbial communities in the ecodynamic of the pollutants (source, transfer, degradation, transformation). It is a multidisciplinary scientific endeavor at the crossroad between microbial ecology, microbial toxicology, physics and chemistry (Fig. 1). It responds to an increasing demand worldwide of the politics and society because of the threat on environmental and human health caused by intense anthropogenic activities. In the context of the Anthropocene, microbial ecotoxicology seeks not only to conduct fundamental researches to understand the impact of pollutants on microbial processes and vice versa but also to carry out applied researches to provide tools readily usable by the society to monitor the evolution of the quality of the environment and to restore polluted sites.