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► Seven phenyl derivatives and four flavones were isolated from seagrass Thalassia hemprichii for the first time. ► (S)-Methoxy-(3,5-dimethoxy-4-hydroxyphenyl) ethanediol was a new compound. ► Methoxy flavones and sulphated flavone glycosides could be used as chemotaxonomic marker of Thalassia genus.
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