A simple eco-friendly approach for the hasty synthesis of stable, potent and benign silver nanoparticles (AgNPs) using seagrass, Syringodium isoetifolium was proposed and described here. The UV–Vis, DLS, XRD, AFM, FESEM, EDX and HRTEM analysis highly characterized and confirmed the presence of polydispersed (2–50nm) spherical and stable AgNPs. FT-IR and phytochemical analysis suggested that the proteins act as reducing and also as capping agent. A hypothetical approach using bioinformatics tools revealed that the Phytochrome B protein of S. isoetifolium might be responsible for the biosynthesis of NPs. Furthermore, biosynthesized AgNPs showed magnificent antibacterial activity against thirteen clinical bacterial pathogens with maximum zone of inhibition of 14.3±0.12mm due to their smaller size and longer stability even at minimal nanomolar (nM) concentration. In addition, the MIC and MBC values also suggested the same. Moreover, the percentage of haemolysis (8.49±3.10 to 73.34±1.79%) and haemolytic index revealed the satisfactory biocompatibility of AgNPs that showed less/no haemolysis up to 3nM concentration. Further, the toxicity effect of biosynthesized AgNPs against the brine shrimp, Artemia salina exhibited significantly increasing mortality (13±4.7 to 100%) with LC₅₀ value at 4nM concentration. Thus, the optical property, crystal structure, size, shape, stability, bactericidal activity, cytotoxicity, and biocompatibility apparently proved that the biologically synthesized AgNPs have typical properties of nanomaterials.