Tanichthys albonubes, which was listed as Class Ⅱ protected animal in China's State Key Protected Aquatic Animal List, is a typical representative of the small Danioninae fishes in South China. Aimed at understanding morphological differentiation between populations as well as providing scientific basis for developing conservation strategies of T. albonubes, we investigated the body-form variation using landmark-based geometric morphometric method among 8 wild populations and 2 hatchery populations of T. lbonubes. Frozen anesthetized fresh specimens were then fixed in 95% ethanol, a Nikon D-800 SLR camera was utilized to take standard images of the fixed specimens afterwards. Landmark coordinate values were extracted after samples digitized by image processing and processed by relative warp principal component(RW), grid deformation and discriminant analysis in TPS series software. The 24 RW were then identified using discrimination analysis to differentiate the ten T. lbonubes populations. The result indicated that, the 1 st, 2 nd and 3 rd RW accounted for 48.20%, 23.12% and 14.83% of the total variation respectively, of which type Ⅱ landmarks 12, 13, 14 and 15 had important contributions, and could explain the most variations. The most morphological variations were displayed in eye diameter and head shape. Furthermore, it uncovered obvious morphological variation among wild populations and hatchery populations. Therefore, we suggest that it should be forbidden to release the hatchery populations in filed. Given the results in this study and the punctate distribution of T. albonubes, we also proposal that the 7 wild populations (expect Vietnam) should be regard as 7 management units(MU), respectively.