Abstract: Carbon and nitrogen content, and stable isotope composition in Spartina alterniflora, Phragmites australis, and Cyperus malaccensis were measured within three wetland system. The results showed that there were significant differences between the invasive species S. alterniflora, a C₄ plant and native species of P. australis, and C. malaccensis based on the indexes of carbon content, C/N value, and the δ¹³C value (-23.83‰)and δ¹⁵N value (6.56‰) in sediment. The impact of the alien species S. alterniflora on the sediment microbes relying on increase in rhizomatic density, significantly enhancing the species diversity and enzymatic activity of the tidal zone sediment microbes, which clearly demonstrated the impact S. alterniflora can have on the carbon and nitrogen cycles within the wetland ecosystem. Results suggest countermeasures should be taken to control the expanding growth of the invasive species. Based on the δ¹³C values of P. australis, and C. malaccensis determined in this study, the P. australis growing at Pearl River estuary is a C₃ plant, meanwhile C. malaccensis is a C₄ plant. The results provide basic data for further studying on the carbon and nitrogen cycles of these three wetland plants/soil system.