The coast of Southeast Indian and the tropical part of the Western Pacific is a habitat for the tropical sea grass Enhalus acoroides. In Ekas Bay, East Lombok, E. acoroides grows well in seashores, which is important to tropical marine ecosystem. Previous research reported the pharmacological activity of E. acoroides such as antioxidant and antibacterial. E. acoroides was tested to identify their secondary metabolites using phytochemical screening. The secondary metabolites were further characterized using thin layer chromatography with specific spray reagent. The phytochemical screening identified primary metabolites such as carbohydrates and proteins. On the other hand, the phytochemical screening also detected secondary metabolites such as alkaloid, phenolic, tannin, saponins, flavonoid, monoterpenes, and sesquiterpenes. The TLC profile with specific spray reagent confirmed the bioactive components such as phenolic, flavonoid, and terpenes in methanol extract of E. acoroides. These results had a significant impact on profiling the marine plant as a new drug candidate. The information of secondary metabolites from E. acoroides will contribute to further research in determination of antioxidant, and antibacterial activity of E. acoroides, as a promising marine drug candidate from Indonesia.