Soil salinization has rapidly encroached from the coastline to inland areas over the past two decades in the Yellow River Delta (YRD). Soil samples were collected from low- (LSW), medium- (MSW), and high- (HSW) salinity wetlands at a depth of 0–20 cm for 16S rRNA sequencing and bioinformatic analyses. The richness and α-diversity indices were significantly lower in saline soils (ECe > 15 dS/m, HSW) than in soils those were not saline (ECe 4) among LSW, MSW, and HSW, respectively, implying that they can serve as bioindicators of soil salinization. Redundancy analysis, Spearman correlation analysis, and the Mantel test suggested that salinity parameters (EC, Na+, K+, Mg2+, Ca2+, Cl−, and SO42−) prominently structured the bacterial community in the current study. These results suggest that the changes of bacterial composition would be induced in these LSW and MSW soils once seawater intrusion occurs. © 2020 John Wiley & Sons, Ltd.