The deep sea, encompassing ocean depths below 200 m which covers more than 70% of the Earth’s surface, represents one of the largest ecosystem in the planet earth. This expansive and largely uncharted environment is home to an extraordinary diversity of life forms, particularly within benthic communities that inhabit the ocean floor. Despite its vast expanse and ecological significance, the deep-sea benthic ecosystem remains one of the least understood environments on our planet. These benthic organisms are not merely passive inhabitants of their surroundings; they play pivotal roles in deep-sea ecosystems, significantly contributing to critical ecological processes such as nutrient cycling, carbon sequestration, and the sustenance of food webs. Despite their importance, the complexities and dynamics of these communities remain poorly understood, highlighting the urgent need for comprehensive research to elucidate their functions and interactions within the broader context of deep-sea ecology. Indian Ocean, the third largest Ocean, is a significant oceanic basin characterized by diverse deep-sea habitats that harbor an array of benthic diversity. This review aims to provide a comprehensive overview of deep-sea benthic biodiversity (meio, macro, and megafauna) in the Indian Ocean, highlighting the critical need for further research to understand and protect these unique and valuable ecosystems while studying the impact of climate change. Furthermore, we discuss the challenges and opportunities associated with studying deep-sea biodiversity in the Indian Ocean, including the development of innovative technologies and the integration of multidisciplinary approaches.