Ailia coila (Hamilton, 1822) commonly called as Gangetic ailia is a "Near Threatened" species in the IUCN Redlist. Samples for the present study were taken from Ganga (Samudragarh and Farakka) and Brahmaputra (Dhubri and Guwahati) river systems. The landmark based truss network system was employed to delineate the stock this species. The truss network was constructed by using 12 landmarks and 25 truss distances were extracted. The first three factors revealed the total variance of 74.53% and the morphological difference between the stocks of this species was related to oblique depth measurement on the dorsal and anal fin, and also on the caudal peduncle region. The difference in body morphology is due to the different in water current pattern, turbulent water and site-specific differences. Discriminant function analysis was employed to reveal the percentage correctly classified individuals on the respective locations. Overall classification rate is found to be good around 97.85%. The results from this present study reveals the existence of difference stock in Ganga and Brahmaputra and it forms a baseline study for the stock-specific management measures. Further, genetic population structure of this species should be studied using molecular markers to validate the results.