Background <p>In protected vegetable cultivation, shading is commonly used to alleviate high light stress by reducing light intensity. However, the effects of shading on the structure and composition of soil microbial communities remain unclear.</p> Methods <p>To compare the effects of no-shading and shading conditions on bacterial and fungal communities in the tomato rhizosphere, high-throughput sequencing was performed on the 16S rRNA gene and the internal transcribed spacer (ITS) amplicons.</p> Results <p>The results showed that the alpha diversity of the fungal community and the Shannon index of bacteria were reduced by shading. The relative abundances of photoautotrophic microorganisms (such as the phylum Cyanobacteria and its class Cyanophyceae) was significantly reduced, while the relative abundance of the class Agaricomycetes was significantly increased. Notably, shading increased the relative abundances of microbial groups known to be associated with plant performance and soil nutrient transformation, such as <i>Sphingomonas</i>, <i>Pseudomonas</i>, and <i>Mortierella</i>. In contrast, the relative abundance of the potential plant pathogenic fungus <i>Gibberella</i> decreased.</p> Conclusion <p>Overall, shading altered the composition of the tomato rhizosphere microbial community by enriching specific groups while inhibiting potential pathogenic and photoautotrophic microorganisms. This study investigated the response of rhizosphere microorganisms to shading from a microbiological perspective, providing a scientific basis for optimizing light environment management in facility cultivation.</p> Graphical Abstract <p></p>