Coral reefs, as we know, are among the most diverse ecosystems, including roughly 25% of marine eukaryotic and prokaryotic species in no more than one percent of the ocean surface area (Miguel et al.,2020). Corals play important role for the ecological products and services they facilitate to marine tropical and subtropical nations. For such a diversity in the life, Environmental DNA or eDNA from environmental samples has the potential to address many of the biodiversity monitoring challenges by obtaining information about species, populations and communities. Whereas, Lakshadweep Islands are also called coral islands by its origin, which stress on the importance to record the biodiversity over the region.