Abstract: Benthic animals play a crucial role as bioindicators of wetland health, significantly contributing to ecosystem stability and serving as essential components in the monitoring of aquatic environments. These organisms respond sensitively to environmental changes, making them valuable for assessing the ecological status of freshwater and marine habitats. Their presence, diversity, and abundance can reflect water quality, pollution levels, and overall ecosystem health. However, traditional benthos surveys rely heavily on morphological identification, a method that is not only time-consuming and labor-intensive but also requires specialized taxonomic expertise. Conducting large-scale, high-frequency, and high-efficiency benthic surveys is challenging, particularly in remote and ecologically sensitive regions such as the Qinghai-Xizang Plateau. The extreme environmental conditions of this region, including high altitude, low oxygen levels, severe temperature fluctuations, and rugged terrain, further complicate field sampling, making it difficult to obtain comprehensive and timely data on benthic biodiversity. In response to these challenges, environmental DNA (eDNA) metabarcoding has emerged as an innovative and highly effective tool for biodiversity assessment and environmental monitoring. This technique utilizes high-throughput sequencing to analyze genetic material present in environmental samples such as water and sediment. By targeting specific DNA barcodes, eDNA metabarcoding allows for the rapid and accurate identification of multiple species or taxa without the need for direct specimen collection or extensive taxonomic expertise. Compared to traditional survey methods, eDNA metabarcoding offers several advantages: it is faster, more precise, non-invasive, and highly objective. Moreover, it enhances the detection of rare, cryptic, or elusive species that may be overlooked using conventional sampling techniques, thereby improving the comprehensiveness of biodiversity assessments. The application of eDNA metabarcoding in benthic biodiversity assessment has gained significant attention in recent years. This approach has been successfully implemented in various aquatic ecosystems, including freshwater, marine, and wetland habitats, to monitor species composition, track invasive species, and assess the impacts of environmental changes. On the Qinghai-Xizang Plateau, where extreme conditions and logistical constraints hinder traditional survey efforts. eDNA metabarcoding presents a groundbreaking alternative for efficient and reliable biodiversity monitoring. By overcoming the limitations of conventional methods, this technology provides a more effective way to understand and protect fragile wetland ecosystems. This paper explores the development, methodologies, and applications of eDNA metabarcoding in benthic biodiversity assessments and environmental monitoring. It highlights the advantages of employing this technique under the harsh environmental conditions of the Qinghai-Xizang Plateau and discusses its future potential. By integrating eDNA technology into wetland conservation strategies, researchers and policymakers can make better-informed decisions to ensure the sustainable management and protection of these critical ecosystems. Ultimately, this study aims to contribute to broader ecological conservation efforts and environmental management initiatives on the Qinghai-Xizang Plateau.