The intraspecific morphological variations of the butter catfish, Ompok bimaculatus has been assessed from two fish farms viz., Chanchra Fish Farm, Jashore (CFFJ) and Fish Seed Complex, Khulna (FSCK) and two natural wetlands viz., Bohni beel, Gopalganj (BBG); Dakatia beel, Khulna (DBK) in the south-western part of Bangladesh. A total number of 80 samples were collected comprising 20 individuals from each sampling location. Five meristic characters, 18 morphometric characters and 21 truss-based morphometric characters were measured respectively. Meristic, morphometric and truss-based morphometric characters were exposed to one-way analysis of variance followed by Tukey-HSD post-hoc test at 5% significance level. Significant differences were observed in two meristic characters viz., CFR and PevFR, and five morphometric and four truss morphometric characters. However, morphometric and truss measurements showed highly intermingled among four populations in discriminant functions (DFs) analysis and discriminant space as well. DFs showed that 6-7, PrDL, HL, PSDL, 1-2, 4-6, FL, ED, 3-9, 5-6, SnL and 4-5 characters contributed 62.8% in first DF, while 2-9, HD, 1-9, 2-3, 2-6, 3-6, 3-4, LAB, 3-8, 9-10, IO and MXBLR characters contributed 20.6% in second DF, and the remaining characters contributed 16.6% in third DF. In cluster analysis, two distinct clusters were made, where BBG demonstrated a solitary group, and FSCK and CFFJ jointly shaped alternative clusters, while the DBK population found a subgroup with CFFJ. These results postulate the occurrence of intermingling populations of this species from four aquatic habitats. These morphological discrepancies play an important role in establishing proper decisions in order to achieve appropriate management and conservation as well as mass seed production for their future sustainability.