Facility agriculture is an efficient way to solve the problem of food supply in China. However, it tends to lead to deterioration of soil health, such as the occurrence of continuous cropping obstacle, which in turn, triggers decline in yield and quality of the vegetables in facility agriculture. Interplanting is an effective way to avoid continuous cropping obstacle. Numerous reports have been published on positive effects of interplanting of vegetables on vegetable production, but few are available on effect of interplanting of vegetable with edible fungi, let alone papers on its underlying mechanisms, such as soil microbiological mechanism. For this purpose, a tomato-agaricus bisporus interplanting experiment was laid out. Tomato is a thermophilic and photophilic species of plant while agaricus bisporus prefers to grow in dark environment. Therefore the latter can flourish in the shade of the former. From the angle of gas exchange, tomatoes can get more CO₂ for photosynthesis from respiration of agaricus bisporus, while agaricus bisporus can have more O₂ generated from tomato in photosynthesis to decompose cultural media into nutrients available to tomato for growth. It is, therefore, hypothesized that the relationship of mutual benefit between tomato and agaricus bisporus should contribute to improvement of crop yield and soil quality in facility agriculture. In the interplanting experiment, tomato seeds were sown in vermiculite for seedling culture. Thirty days later, the seedlings were transplanted into pots, 2 seedlings each planted in diagonally opposite corners and a ditch was dug in between the two plants for culturing of agaricus bisporus. The experiment was designed to have three treatments, each having three replicates; i.e. Treatment L (control without addition of any mushroom culturing media or inoculation of mushroom spores in the ditch); Treatment LS (mushroom culturing media added, but no mushroom spores inoculated); and Treatment LSA (mushroom culturing media added and mushroom spores inoculated). Biomasses of tomato plants, fresh weight of fruits and nitrate contents therein from different treatments were measured for analysis of effects of the interplanting on yield and equality of the tomato. For the microbial mechanisms, real-time quantitative PCR and PCR-DGGE fingerprinting analyses of targeting soil bacteria and fungi were conducted to determine numbers of copies of 16S and 18S rRNA genes and community compositions. Results show that Treatment LSA significantly increased tomato biomasses (p<0.05) and was the highest in fruit yield, but the lowest in nitrate content in tomato among the treatments. Though the numbers of gene copies of soil bacteria and fungi did not vary much statistically in the soil under the interplanting as compared those in the control, they were the highest in Treatment LSA. The PCR-DGGE fingerprinting profiles reveal that the treatments differed slightly in composition of soil bacterial community, but the PCR-DGGE fingerprinting profiles of the fungal 18S rRNA genes show that Band 4 and Band 6 were obviously lower in intensity in Treatment LSA than in the other two treatments. Cluster analysis indicates that Treatment LSA differed significantly from the other two in soil fungal community composition, that is, in Treatment LSA differentiation occurred in fungal community structure. Moreover, principal component analysis of the changes in soil fungal community structure in different treatments shows that along the X axis (primary principal component), Treatment LSA deviated from the other two and along the Y axis (secondary principal component), Treatment L parted apparently from Treatment LS, indicating that Treatment LSA had some apparent impact on community structure of the dominant soil fungi. By sequencing and constructing phylogenetic tree, it was found that Band 4 and Band 6 that decreased significantly in intensity in the DGGE fingerprinting profiles were affiliated with Fusarium oxysporum and Nigrospora respectively, both of which were documented as pathogens. All in all, the findings suggest that interplanting of tomato with agaricus bisporus may reduce the incidence of some soil borne diseases by inhibiting certain pathogenic microbes, thus contributing to improvement of yield and quality of the crops and soil quality as well.