Aims: This investigation is designed to evaluate the antibacterial efficiency of the noodle grass Syringodium isoetifolium, which is commonly found in the Indian coastal waters. Also, this study characterizes the active compound and predicts the mode of action in silico. Methods and Results: Human pathogenic bacteria were treated with crude metabolites of S. isoetifolium. The potent fraction b was analysed by UV/VIS, Spectroscopy RP-HPLC, FT-IR, ESI-Mass and H-1 and C-13 NMRs and determined to be a hydrate of pheophytin a (C55H74N4O6). The isolated compound Pheo had MIC values of 6.2 +/- 0.7 (Salmonella typhi) and 12.5 +/- 0.8 (Escherichia coli and Pseudomonas aeruginosa) mu g ml(-1). Molecular docking studies of the compound were done to find the binding sites on the pathogens using a Molegro Virtual Docker platform. Pheo targets umuC proteins by binding compactly to five amino acid residues with interaction energy of -3.66 and a Moldock score of -160.175. Conclusions: Hence, we conclude that pheophytin a, besides being an accessory photosynthetic pigment, also has proven to be antibacterial against human pathogens. Lesser MIC values with definite binding sites predicted in silico are suggestive of a precise of action for this compound. Significance and Impact of the Study: Easy extraction methods of the active compound that has a definite target render this under-explored seagrass a good source of antibacterial compound against human pathogenic bacteria. This learning may favour more researches in this unexplored area to build up Pheo-based natural products as antibiotic therapies.