In the 1980s, a fishery transplant was carried out nationwide using the H. nipponensis from the Yalu River system as the source population, which achieved significant economic benefits. However, the genetic diversity of the initial small population established by transplantation has not received due attention due to the subsequent effects of different transplantation behaviors (repeated introduction, mixing of other sources, and unintentional transplantation) and adaptation to the habitat. In this study, 439 individuals were collected from 15 transplanted populations across China’s main production regions (Northeast, North, Northwest and Southwest). Mitochondrial cytochrome c oxidase I (CO I) sequences were used to assess genetic diversity and differentiation. The analysis results showed that a total of 47 haplotypes were detected in 15 populations, Overall haplotype diversity (Hd=0.690) and nucleotide diversity (Pi=0.00290) exhibit species characteristics of high haplotype diversity (Hd) and low nucleotide diversity (Pi). Group Evolutionary Tree, haplotype networks and AMOVA showed that most molecular variance occurred within populations (65.06 %, versus 34.94 % among populations). Populations from Miyun Reservoir (MY) and Panjiakou Reservoir (PJK) in North China formed a separate clade and were highly differentiated from all others (Fst > 0.5), probably reflecting repeated introductions from native Japanese sources. The Dahushi Reservoir (DHS) population showed marked diversity loss, likely attributable to accidental transplantation of a very small founder group. The diversity levels of the four populations in Northeast China, which are connected to the water system of their source areas, are relatively balanced. The populations in Northwest and Southwest China, exhibit moderate to high levels of diversity, which demonstrated the potential adaptation of fish species to the new habitat. Neutrality tests, mismatch distributions and Bayesian skyline plots all indicated a historical population expansion. Based on the current research results, it is recommended to identify the biological management units and core population germplasm resources in China as soon as possible, implement necessary genetic monitoring in a timely manner, and then carry out orderly germplasm use strategies, block based resource management, and fishery production management measures to promote the sustainable and healthy development of the industry.