Abstract: To explore the influence of Scrophularia ningpoensis and tobacco planting on bacterial community structure in soil under different planting patterns, we used Illumina MiSeq technology to identify bacteria in soil. It was found that the richness and diversity of bacterial species in S. ningpoensis soil tended to be higher than in tobacco soil, but differences were not statistically significant. Crop species and planting pattern both affected the abundance and the order of dominant bacteria. At phylum level, presence of Saccharibacteria in tobacco soil was significantly higher than that in S. ningpoensis soil, whereas presence of Gemmatimonadetes in S. ningpoensis soil was significantly higher than that in tobacco soil. Bacteroidetes occurrence also varied between different planting patterns. At genus level, taxa significantly more common in tobacco soil than in S. ningpoensis soil, included unclassified Xanthomonadaceae, norank Saccharibacteria, uncultured Gaiellales, and norank SC-I-84. Meanwhile, for S. ningpoensis soil, significantly more common taxa (than in tobacco soil) included norank GR-WP33-30, norank JG30a-KF-32, Gemmatimonas, Candidatus_Solibacter, uncultured Nitrosomonadaceae, norank C0119, norank Subgroup_6, norank DA101_soil_group, norank BIrii41, Anaeromyxobacter, unclassified Xanthomonadales, uncultured Methylophilaceae, and norank JG37-AG-20. Planting pattern had almost no effect on genera detected. Principal component analysis also showed that crops had a greater influence than planting patterns. In summary, soil bacteria community structure differed between tobacco and S. ningpoensis crops, and was also affected to a lesser extent by planting pattern. Hence, in an intercropped field the microbial community displays spatial heterogeneity determined by the crop species.