【Background】 Spartina alterniflora Loisel, originally distributed along the Atlantic coasts of North America and the Gulf of Mexico, has been introduced into many countries including China, and has often become invasive, causing significant changes in both the structure and functioning of coastal ecosystems. The invasion mechanism and control strategies against this species constitute an important problem in current invasion ecology. S.alterniflora is rich in flavonoids, which may explain the fast expansion of the species. Since flavonoids are also of Spartina-originating flavonoids as well as collection of Spartina biomass has been suggested a way of controlling the invasion of the species. 【Method】Using rutin as standard, total flavonoid concents in different organs of S.alterniflora were compared by reaction with NaNO2 and Al(NO3)3. We also examined the relationship between flavonoids contents in winter shoots and their position in coastal saltmarsh. Using a L9(34) orthogonal test, the extraction method of flavonoids from stored, dry S.alterniflora leaves was also optimized. 【Result】 Leaves of S.alterniflora contain the highest amount of flavonoids, while lower levels were found in roots, rhizomes, stems, leaf sheath, glumes and seeds. Flavonoid contents in winter shoots from coastal saltmarsh decreased as the plants grew further from the sea towards upland. The best extraction method for flavonoids from S.alterniflora involved the following parameters: 1∶30 (g∶mL) material∶solvent ratio, using 70% alcohol as solvent, and extraction in water bath at 80 ℃ for 2 h. 【Conclusion and significance】Various parts of S.alterniflora, especially leaves, contain high levels of flavonoids, which may positively correlated with their closeness to the seaside parts of coastal ecosystems. Further research on the role of flavonoids may throw light on the invasion mechanism of S.alterniflora. The value of flavonoids as medicine may stimulate the active harvesting of Spartina biomass, which could become a potential strategy in controlling its invasion.