Abstract: The establishment of national aquatic germplasm reserves is critical for encouraging harmonious cohabitation of man and nature, protecting national food security and preserving biodiversity. Under the background of the "ten-year ban on fishing in the Yangtze River", revealing the spatial distribution characteristics and driving factors of the national aquatic germplasm reserves can help protect the aquatic germplasm resources in the Yangtze River Basin effectively. The kernel density estimation approach was used in this research to investigate the spatial and temporal evolution characteristics of 231 national aquatic germplasm reserves in the Yangtze River Basin. On this premise, an optimal parameter-based geodetector was presented to optimally discretize the factors and discover the Yangtze River Basin's primary driving forces and mechanisms. The entropy weight approach was paired with K-means clustering to investigate the differentiation patterns of each prefecture-level city in terms of the density of reserves, physical geography, socio-economics, and environmental pollution and governance, in order to provide theoretical support for the development, construction, and management of aquatic germplasm reserves in China. The following were the primary conclusions: firstly, national aquatic germplasm reserves in the Yangtze River Basin were spatially aggregated, with a high degree of geographical concentration and a high degree of inter-regional imbalance, exhibiting a spatial distribution density evolution pattern of "single-core agglomeration-triple-core agglomeration-multi-polar multi-zone". Secondly, the national aquatic germplasm reserves in the Yangtze River Basin were developed as a result of a mix of natural environmental conditions and economic and societal influences. Natural environmental elements, economic and social considerations, played roles in the spatial aggregation pattern of reserves. Among which, economic and social factors had a greater impact. Thirdly, there existed diverse distribution features in the numerous prefecture-level cities in the Yangtze River Basin, which needed to be protected in differential ways.