Abstract Populations of the Halophila ovalis (R.Br) Hook. f—H. minor (Zoll.) den Hartog complex differ in the occurrence of sulfated flavonoids. In the Western Pacific, plants with larger leaves and/or more pairs of cross veins in the blades contain sulfated flavonoids, but those with smaller leaves and/or fewer cross veins lack these compounds. In the Indian Ocean, sulfated flavonoids are produced by smaller-leaved populations of Thailand, Tanzania and Madagascar, but are absent from smaller-leaved populations of India and South Africa. Among the larger-leaved populations of the Indian Ocean, those of India, Sudan and Saudi Arabia contain the sulfated flavonoids, but those of Thailand do not contain these compounds. Among the populations that contain sulfated flavonoids, most contained four compounds, but the small-leaved plants of Tanzania and Madagascar differed and produced only one sulfated flavonoid. The H. ovalis—H. minor complex remains one of the most complicated of the groups of seagrasses because of the wide range of morphological and chemical variation among local populations.