| Summary: | The Red Sea is one of the most biodiverse aquatic ecosystems. Notably, seagrasses possess a crucial ecological significance. Among them are the two taxa <i>Halophila stipulacea</i> (Forsk.) Aschers., and <i>Thalassia hemprichii</i> (Ehrenb. ex Solms) Asch., which were formally ranked together with the genus Enhalus in three separate families. Nevertheless, they have been recently classified as three subfamilies within Hydrocharitaceae. The interest of this study is to explore their metabolic profiles through ultra-high-performance liquid chromatography-high-resolution mass spectrometry (UPLC-HRMS/MS) analysis in synergism with molecular networking and to assess their chemosystematics relationship. A total of 144 metabolites were annotated, encompassing phenolic acids, flavonoids, terpenoids, and lipids. Furthermore, three new phenolic acids; methoxy benzoic acid-<i>O</i>-sulphate (<b>16</b>), <i>O</i>-caffeoyl-<i>O</i>-hydroxyl dimethoxy benzoyl tartaric acid (<b>26</b>), dimethoxy benzoic acid-<i>O</i>-sulphate (<b>30</b>), a new flavanone glycoside; hexahydroxy-monomethoxy flavanone-<i>O</i>-glucoside (<b>28</b>), and a new steviol glycoside; rebaudioside-<i>O</i>-acetate (<b>96</b>) were tentatively described. Additionally, the evaluation of the antidiabetic potential of both taxa displayed an inherited higher activity of <i>H. stipulaceae</i> in alleviating the oxidative stress and dyslipidemia associated with diabetes. Hence, the current research significantly suggested <i>Halophila</i>, <i>Thalassia</i>, and <i>Enhalus</i> categorization in three different taxonomic ranks based on their intergeneric and interspecific relationship among them and supported the consideration of seagrasses in natural antidiabetic studies.
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