The South China Sea and the Indo-Pacific Coral Triangle, two of the most ecologically significant regions on Earth, are intricately connected in terms of environmental and biological diversity. The South China Sea stands out as a global hotspot for marine biodiversity, hosting an unparalleled array of habitats that support an incredibly diverse range of species. The tropical and subtropical marine environments found in these regions offer ideal conditions for the proliferation and sustenance of a wide variety of marine life forms, contributing to the richness of China's marine biodiversity and serving as a vital repository of marine resources. Within marine ecosystems, marine bacteria play a crucial role in driving ecosystem processes and maintaining ecological balance. This study can gain valuable insights into the biodiversity of the Western Pacific and the Indo-Pacific convergence zone, by studying deep-water bacteria in the South China Sea. Through the analysis of water samples collected from deep-sea sites in the South China Sea as part of an open research initiative, the analysis result have been able to uncover the intricate diversity and composition of deep-sea marine bacterial communities using advanced high-throughput sequencing techniques for 16S rRNA gene sequencing. The results of this study revealed a remarkable diversity of bacterial taxa present in the deep-sea waters of the South China Sea, encompassing 15 phyla, 20 classes, 24 orders, 86 families, 140 genera, and 150 species. Among these, several dominant genera such as Paenibacillus, Bacillus, Thalassospira, Methylophaga, Bacteroides, Gracilibacillus, Oceanobacillus, Idiomarina, Oleiphilus, and Alcanivorax were identified, each with unique characteristics and potential applications in various fields including biotechnology, biofuel production, and environmental remediation. Furthermore, specific species of deep-sea bacteria such as Lentibacillus amyloliquefaciens, Pseudomonas stutzeri, Alcanivorax dieselolei, Halolactibacillus miurensis, and Dietzia maris have been recognized for their potential in antibiotic production, bio control, oil degradation, and denitrification processes. The identification of these valuable bacterial strains underscores the importance of exploring and harnessing the biological resources present in the South China Sea for sustainable development and environmental conservation. Through the application of high-throughput sequencing technologies, this study have unveiled the distinct flora characteristics and diversity of deep-water bacteria in the South China Sea, highlighting their immense potential for biological exploitation and utilization. These findings not only enrich our understanding of marine biodiversity in this region but also pave the way for the discovery of novel bioactive compounds, biotechnological innovations, and sustainable solutions for addressing environmental challenges. The study conducted in the South China Sea serves as a testament to the invaluable insights that can be gained from studying the microbial communities in our oceans and underscores the importance of preserving these unique ecosystems for future generations.