Abstract: Objective: To compare the content of flavonoids and total alkaloids in the seed of Nitraria from Inner Mongolia.Methods: The total flavonoids were extracted by soxhlet extraction, and were determined by Al ( NO3) 3-NaNO2spectrophotometry method.Total alkaloids in Nitraria was extracted by acid- base and the content of total alkaloids was determined by the acidic dye colorimetry.Results: It showed the content of flavonoids and total alkaloids in fruits and leaves of Nitraria was significantly different ( p < 0.05) .Fruits of Nitraria sibirica Pall.and leaves of Nitraria sphaerocarpa Maxim had the highest content of flavonoids, and Nitraria tangutorum Bobr. had the highest content of total alkaloids. Conclusion: The research provided some reference for screening alopecuroides and quality evaluation of the germplasm resources.