Halophila johnsonii Eiseman is a shallow-water marine angiosperm which contains UV-absorbing metabolites. Studies on methanol extracts of H. johnsonii by means of HPLC–UV, NMR, HPLC–MS resulted in isolation and identification of seven previously unknown flavone glycosides: 5,6,7,3′,4′,5′-hexahydroxyflavone-7-O-β-glucopyranoside (1), 5,6,7,3′,4′,5′-hexahydroxyflavone-7-O-(6″-O-acetyl)-β-glucopyranoside (2), 6-hydroxyluteolin-7-O-(6″-O-acetyl)-β-glucopyranoside (3), 6-hydroxyapigenin-7-O-(6″-O-acetyl)-β-glucopyranoside (4), 6-hydroxyapigenin-7-O-(6″-O-[E]-coumaroyl)-β-glucopyranoside (5), 6-hydroxyapigenin-7-O-(6″-O-[E]-caffeoyl)-β-glucopyranoside (6) and 6-hydroxyluteolin-7-O-(6″-O-[E]-coumaroyl)-β-glucopyranoside (7). Also isolated were three known flavone glycosides, 6-hydroxyluteolin 7-O-β-glucopyranoside (8), scutellarein-7-O-β-glucopyranoside (9), and spicoside (10), and five known flavones, pedalitin (11), ladanetin (12), luteolin (13), apegenin (14) and myricetin (15). Qualitative comparison of the flavonoid distribution in the leaf and rhizome-root portions of the plant was also investigated, with the aim of establishing the UV-protecting roles that flavonoids played in the sea grass.