Seagrass phenophases are crucial in understanding their reproductive biology but are seldom documented. We studied flowering and fruiting phenophases of Enhalus acoroides from a mixed-species intertidal seagrass meadow in Ritchie’s archipelago, Andaman Islands, India. The estimated mean densities of pistillate and staminate flowers were 16.0 ± 12.0/ m2 and 12.7 ± 7.3/ m2, respectively. We observed the bloom of free-floating male flowers (961.7 ± 360.4/ m2) during the spring low tides (at mean sea surface temperature ~30°C). Seagrass cover, shoot density, and canopy height of E. acoroides, along with flowering densities, showed a zonal variation within the sampled meadow. We report the first-time observations of several phenophases of E. acoroides, such as female inflorescence buds, male inflorescence, a bloom of released male flowers, pollination, and fertilized flowers from the Indian waters. We also report the prevailing threats to seagrass meadows, such as meadow scarring done by boat anchorage in the Andaman Islands.