With the extensive production and application of black phosphorus (BP) nanosheets, release to the environment is inevitable, which raises concerns about the fate and effects of this two-dimensional (2D) material on sensitive receptors such as environmental microbes. Although the bacterial toxicity of BP nanosheets has been demonstrated, whether the biological response differs in pathogenic and nonpathogenic strains of a microorganism is unknown. Here, enteropathogenic Escherichia coli (EPEC) and nonpathogenic Escherichia coli DH5α (E. coli DH5α), Escherichia coli k12 (E. coli k12), and Bacillus tropicus (B. tropicus) are used to comparatively study the microbial toxicity of BP nanosheets. Upon exposure to BP nanosheets across a range of doses from 10 to 100 μg mL −1 for 12 h, EPEC experienced enhanced growth and E. coli DH5α and E. coli k12 were not affected, whereas B. tropicus exhibited clear toxicity. By combining transcriptome sequencing, proteome analysis, and other sensitive biological techniques, the mechanism of BPinduced growth promotion for EPEC was uncovered. Briefly, BP nanosheets activate the antioxidation system to resist oxidative stress, promote protein synthesis and secretion to attenuate membrane damage, enhance the energy supply, and activate growth-related pathways. None of these impacts were evident with nonpathogenic strains. By describing the mechanism of strain-dependent microbial effects, this study not only highlights the potential risks of BP nanosheets to the environment and to human health but also calls attention to the importance of model strain selection when evaluating the hazard and toxicity of emerging nanomaterials.