Abstract: 【Objective】 This study aimed to elucidate the morphological differences between wild-caught and farmed populations of Thamnaconus septentrionalis and establish an efficient identification method， providing theoretical basis for conservation and sustainable utilization of Thamnaconus septentrionalis germplasm resources. 【Method】 The traditional morphological method and geometric morphometric method based on landmark points were used to analyze the morphological differences of 120 Thamnaconus septentrionalis samples of wild-caught populations in Qingdao， Shandong and Zhoushan， Zhejiang， and farmed populations in Yantai， Shandong and Lianyungang， Jiangsu. 【Result】 The traditional morphological analysis showed that there were marked differences in 28 measurable proportional morphological traits among the 4 populations. Principal component analysis extracted 8 principal components with a cumulative contribution rate of 81.37%， and the scatter plots of the populations overlapped. Cluster analysis showed that the wild-caught populations from Qingdao and Zhoushan were the most similar in morphology， while the farmed population from Lianyungang was the most distant from the others. The cross-validation discrimination accuracy and stepwise discriminanation accuracy were 90.00% and 83.33% respectively. The geometric morphometric analysis showed that the cumulative contribution rate of the 6 principal components extracted based on 14 landmark points was 84.11%， and the cumulative contribution rate of the first and second canonical variables was 94.12%. The principal component analysis results indicated that the farmed population from Lianyungang was more distinct from the others， while the farmed population from Yantai overlapped more with the wild-caught populations， but the overall discrimination effect was clearer than that of traditional morphology. The Mahalanobis distance and Procrustes distance between the two wild-caught populations were the shortest. The comprehensive discrimination accuracy and cross-validation discriminantion accuracy were increased to 93.33% and 89.17% respectively. The thin-plate spline analysis showed that the morphological differences between wild-caught and farmed populations were concentrated in the head， the anterior and middle part of the trunk， and the tail. Among them， the farmed population in Lianyungang had the greatest divergence， and although the two wild-caught populations were morphologically similar， the variation parts were polymorphically distributed. 【Conclusion】 Morphological differentiation is found in the head， the anterior and middle part of the trunk， and the tail between wild-caught and farmed Thamnaconus septentrionalis populations. Such differentiation is a phenotypic response to the combined effects of complex environmental factors in natural waters （such as water flow and feeding）， the farmed environment， and artificial directional selection. Geometric morphometric methods have unique advantages in identifying subtle morphological variations and visualization， and can be used as a precise tool for identifying populations and assessing the differences in germplasm resources.