Abstract: Herbicide that applied to agriculture can contaminate estuarine and costal ecosystems through overspray, ground-water leachate and runoff to impair the health of seagrass and seaweed. This study investigated the toxic effects of herbicide atrazine (1 μg/L, 5 μg/L and 25 μg/L) and prometryn based on the photosystem II (PSII) inhibition on four species of seagrass (Zostera marina, Z. caespitosa, Z. japonica and Phyllospadix iwatensis M.) and 2 species of seaweed (Ulva lactuca L., Nemalion helminthoides) in north China. Results showed that the maximum quantum yield of Z. japonica. U. lactuca L., N. helminthoides and Z. marina L seedlings depressed significantly at 1 μg/L prometryn and 5 μg/L atrazine after 72h exposure, and Z. marina, Z. caespitosa and P. iwatensis depressed at both 5 μg/L prometryn and atrazine. At the same concentration, prometryn showed higher toxicity than atrazine for all species. Z. japonica and the two seaweed were more sensitive to herbicide then others.