Beardless barb, Cyclocheilichthys apogon (Valenciennes, 1842) is a freshwater fish of importance as source of low-cost protein in Lower Mekong Region. The present study applied multivariate morphometric technique to identify fishery management units of C. apogon from six populations of three different river drainages: Pong, Chi, and Mun Rivers. Thirty-two truss measures and standard length were obtained using digital calliper from 291 fish individuals, and raw measured data were then subjected to allometric equation to remove size-dependent variation prior further statistical analyses. Multivariate analysis of variance (MANOVA) indicated highly significant differences in morphometric characters between populations (p <0.01). The first three principal axes of principal component analysis (PCA) explained 49.29% of total variance. The PCA also revealed that morphological variations related to the characters of head depth, body length, body depth, caudal peduncle length and depth. In discriminant function analysis (DFA), the first two discriminant functions accounted for 72.00% of total variation, and discriminated fish samples into three major groups following to their collecting drainages. Furthermore, 96.29 and 90.56% of fish samples were correctly classified into their respect populations with original and cross-validated tests, respectively. The reliable morphometric variations in the present study suggest that management unit of C. apogon should define relied on the isolation of river drainage. Moreover, the study also indicates the involvement of environmental conditions in morphological adaptation, providing useful information for the sustainable conservation of this fish.