Microbial communities are essential components of natural ecosystems. Of the global oceans, the Indian Ocean remains the least studied in terms of its microbial diversity, despite it being a highly dynamic tropical water body. Metagenomics methods have significantly advanced studies in marine microbial ecology in recent years. Preliminary metabarcoding assessments are recommended to mitigate against the associated costs, prior to the metagenomics study, to give an impression of the diversity expected and determine the sequencing effort required. We report here the first metabarcoding survey of bacterial diversity of the western Indian Ocean (WIO) using samples used for optimizing environmental DNA (eDNA) isolation as pilot experiment for a metagenomic study investigating the coral-reef microbiome of the region. Sampling of water and sediment samples was done near-shore sublittoral and within the coral reef. About 3,000 microbial ribotypes were inferred, from which 41 phyla were uncovered. Sediments registered higher alpha diversity than seawater samples. The phylum Proteobacteria was dominant with its members constituting over 60% of the ribosomal sequence variants (RSVs). The other abundant bacteria were members of Bacteroidetes and Cyanobacteria phyla. We identified bacterial species with potential broad biotechnological applications, underscoring the WIO’s richness and the usefulness of eDNA metabarcoding approaches in bioprospecting as well as monitoring and/or surveying marine ecosystems.