Abstract: In this study, the typical vegetation types(Kandelia candel, Phragmites australis, Cyperus malaccensis) in the Minjiang Estuary were used as the research objects, and the bare flat was used as the control. The 16S rRNA high-throughput sequencing technology was used to explore the diversity of bacteria in the surface soil of different vegetation types. The results showed that 6410 OTUs were obtained from soil samples, belonging to 97 phylas, 191 classes, 359 orders, 468 families, 582 generas and 170 species. At the phylum level, the dominant bacteria were Proteobacteria, Bacteroidota, Cyanobacteria, Firmicutes and so on. The dominant bacteria in the mudflat soil were Cyanobacteria, the K. candel community was Bacteroidota, and the P. australis community and C. malaccensis community were Proteobacteria. At the class level, the relative abundance ratios of Cyanobacteriia and Bacilli were mudflat > K. candel > P. australis > C. malaccensis. At the order level, the dominant order in K. candel and P. australis communities was Flavobacteriales. At the family level, Flavobacteriaceae was the dominant family in the soil of K. candel, P. australis and C. malaccensis, with the relative abundance ratios of 29.60%, 18.02% and 6.17%, respectively. At the genus level, Flavobacterium was the main dominant genus in the three vegetation-covered soils. At the species level, Jeotgalibacillus malaysiensis is a unique species in mudflat. The Observed species, Shannon index and Simpson index of different vegetation communities showed C. malaccensis > P. australis > K. candel > mudflat, and the soil of mudflat was significantly different from that of the three vegetation communities(P < 0.05). The bacterial community and diversity of the Minjiang Estuary wetland show specific environmental preferences based on the presence or absence of vegetation coverage and different types of vegetation coverage.