Wild stocks of endangered mrigal carp, Cirrhinus cirrhosus (Bloch 1795), continues to decline rapidly in the Indo-Ganges river basin. With an objective to evaluate its population status, landmark-based morphometric and meristic variations among three different stocks viz., hatchery (Jessore), baor (Gopalganj) and river (Faridpur) in Bangladesh were studied. Significant differences were observed in 10 of the 15 morphometric measurements viz., head length, standard length, fork length, length of base of spinous, pre-orbital length, eye length, post-orbital length, length of upper jaw, height of pelvic fin and barbel length, two of the 8 meristic counts viz., scales above the lateral line and pectoral fin rays and 10 of the 22 truss network measurements viz., 1 to 10, 2 to 3, 2 to 8, 2 to 9, 2 to 10, 3 to 4, 3 to 8, 4 to 5, 4 to 7 and 9 to 10 among the stocks. For morphometric and landmark measurements, the 1st discriminant function (DF) accounted for 58.1% and the 2nd DF accounted for 41.9% of the among-group variability. In discriminant space, the river stock was isolated from the other two stocks. On the other hand, baor and hatchery stocks formed a very compact cluster. A dendrogram based on the hierarchical cluster analysis using morphometric and truss distance data placed the hatchery and baor in one cluster and the river in another cluster and the distance between the river and hatchery populations was the highest. Morphological differences among stocks are expected, because of their geographical isolation and their origin from different ancestors. The baseline information derived from the present study would be useful for genetic studies and in the assessment of environmental impacts on C. cirrhosus populations in Bangladesh.