For exploring the species and genetic diversity of Suaeda plants in Shanghai coastal wetlands， this paper investigated and studied the species resources and genetic diversity of Suaeda plants collected from 11 stations in three coastal wetlands， including the Nanhui east tidal flat in Pudong New Area， Fengxian tidal flat， and Chongming east tidal flat. The results showed that： （1） By the morphological identification and molecular identification based on ITS and matK sequence barcode analysis， the collected Suaeda plants in Shanghai coastal wetlands were two species： Suaeda salsa and Suaeda glauca. （2） In this study， we found only S. glauca distributed in Chongming east tidal flat， and the genetic distance between these seven samples collected was 0， indicating there was no gene exchange between the population and the outside area. （3） According to ITS and matK sequence analysis of S. salsa distributed in Chongming District， Pudong New Area， and Fengxian District， there are 2-3 haplotypes， respectively， and genetic distances （D） between populations of different districts are smaller than 0.05， indicating that most of them are genetic variations within the population. We further found that the genetic diversity of Fengxian S. salsa population was the lowest on ITS and matK sequences （H_d=0.419±0.113， P_i=0.000 9 and H_d=0.133±0.112， P_i=0.000 4）， while the genetic diversity of Pudong S. salsa population was the highest （H_d=0.629±0.086， P_i=0.001 5 and H_d=0.475±0.141， P_i=0.004 3）. There is moderate differentiation between the S. salsa population of Pudong New Area and both S. salsa populations of Chongming District and Fengxian District （0.05<F_ST<0.15， P<0.05； N_m>1）， while there is high differentiation between the Chongming S. salsa population and the Fengxian S. salsa population （0.15<F_ST<0.25， P<0.05； N_m<1）. This study laid a solid foundation for the protection and population restoration of Suaeda plants in Shanghai coastal wetlands.