Tropical coral reefs are major habitats for marine macroalgae or seaweeds. Macroalgae represent a key functional group among the coral reef communities and perform vital ecological functions like reef structure stabilisation, production of tropical sands, nutrient retention and recycling, primary productivity and trophic support. Coral reef macroalgae are comprised of three major pigment-group-based phyla: Chlorophyta (green algae), Heterokontophyta or Ochrophyta (brown algae) and Rhodophyta (red algae). Green macroalgae or Chlorophyta contain chlorophyll a and b pigments in the same proportion as that of higher plants along with β-carotene and xanthophylls and have significant industrial or commercial value. Chlorophyta members commonly inhabit the littoral zone with strong sunlight. This chapter highlights micro-level habitat preference of green macroalgae or Chlorophyta species sampled from Bet Shankhodhar Reef from the Gujarat coast of India as a unique case study. This study identifies four Chlorophyta species: Halimeda tuna (Ellis & Solander) Lamouroux, Caulerpa sertularioides (S. Gmelin) Howe f. brevipes (J. Agardh) Svedelius, Valonia aegagropila C. Agardh and Valoniopsis pachynema (Martens) Børgesen, as indicator species of the backreef zone. Shallow tidal pools in the backreef zone of Bet Shankhodhar Reef are preferred microhabitats for C. sertularioides and V. aegagropila.