Coastal ecosystems are invaluable mosaics of interconnected habitats that harbor a unique assemblage of organisms that can thrive where oceans meet the land. The most prominent coastal ecosystems include mangroves, salt marshes, coral reefs, and seagrass meadows. These ecosystems are most vulnerable to direct and indirect anthropogenic threats such as overexploitation, habitat degradation, pollution, and climate change. Even though coral reefs and mangroves have received significant attention, more research needs to highlight the importance of seagrass meadows and tidal flats which provide environmentally and economically valuable ecosystem services globally. The tropical Indo-Pacific is known to harbor one of the highest seagrass diversities worldwide, but comparatively few recent assessments have focused on the extent of seagrass meadows in the Indian Ocean countries. Additionally, numerous studies have documented a rapid loss of tidal flats in the Indian Ocean region and have highlighted their vulnerability to the threatening processes occurring in the terrestrial and marine realms. In this review, the importance of the highly productive seagrass meadows and tidal flats forming the foundation of the coastal food web biodiversity in the Indian Ocean is discussed. Examining the status of these ecosystems indicate that conservation efforts are largely focused around areas where active stressors are present or where management actions have been taken to reverse degradation and habitat loss, and several of the complex ecological interactions that exist in such ecosystems have received limited attention. Unfortunately, a lack of international legislation for seagrass management and tidal flat conservation indicates that most protection is typically dependent on local and regional efforts which likely contribute to the ongoing staggering loss of global seagrass biodiversity at a rate of 1.5% per year. The present chapter advocates for the future focus and orientation in research to conduct targeted biodiversity assessment in the Indian Ocean periphery and linking such efforts to the established conservation programs.