Two pepper inbred lines, ‘SJ11–3’, ‘06g19–1–1–1’, and a local variety ‘Zhangshu gang’ were used as materials, also using the Illumina MiSeq 2500 sequencing platform to sequencing the 16S rRNA gene V3 + V4 regions of bacteria and ITS1 region of fungal, in the rhizosphere soil before and after pepper planting. And combining the bioinformatics to analyze the richness, diversity index and community structure of the soil microorganism. The results showed that both Proteobacteria and Acidobacteria were the dominant bacteria in the soil before and after pepper cultivation. Ascomycota, Basidiomycotina and Fusarium were the dominant fungi. The bacteria species in the soil before and after the planting were more abundant and more diversified than the fungi. The relative abundance and community structure of soil bacteria and fungi had changed after pepper planting. The Ace, Chao and Shannon index of soil bacteria was increased,25.26% – 25.49%, 24.51% – 24.87% and 8.28% – 24.87% respectively after pepper planting. The Simpson index of fungi was increased by 78.45% – 78.45%, also Shannon index had a different degree of reduce after pepper planting. The number and types of OTU in soil were also changed after pepper planting, the specific OTU type in soil was reduced, while the number of bacteria OTU was significantly increased 28.73% after pepper planting. The effect of variety difference on OTU type of fungi was greater than that of bacteria, and the relative abundance of pathogenic fungi was significantly increased.