Halophila stipulacea beds in the northern Gulf of Elat (Red Sea) may be subdivided into three different sub-habitats, each harboring a distinct population of diazotrophs. Nitrogen (N2) fixation in the phyllosphere and in the rhizomes/upper-sediment niche was light dependent, suggesting its dependence on photosynthesis. N2 fixation in the phyllosphere was not affected by the addition of either glucose or 3-3,4-dichloro-phenyl-1,1-dimethyl-urea (DCMU), indicating that the diazotrophs involved carried out non-oxygenic photosynthesis. They may, thus, have been photosynthetic bacteria. N2 fixation in the rhizomes/upper-sediment niche, however, was greatly enhanced by the addition of glucose, but was suppressed in the presence of DCMU. This indicates that the diazotrophs involved here probably possess two photosystems (I and II) and may be Cyanobacteria. The anaerobic rhizosphere, in which fixation rates in light were very slow but were greatly enhanced by the addition of glucose, is probably populated by heterotrophic diazotrophs. Plant and sediment samples used in the present study were collected from the Gulf of Elat between 1990 and 1992.