Long-whiskered catfish Sperata aor is a freshwater catfish known for its supreme flesh quality and fast growth, whose captive-reared broodstock denotes a difficult challenge for aquaculture. The reproductive dysfunctions in long-whiskered catfish raised in tank conditions were observed by comparing tissue biochemical composition and ovarian histology of wild female broodstock. Sixty (60) female broodstocks were used in the current study, consisting of 30 reared at sandy-muddy soil tank bottoms in captive conditions and 30 wild individuals collected from the haor basin during the breeding season. The fish reproductive state was investigated using the biometric and reproductive parameters, biochemical composition and levels of amino acids in the different tissues, and histological analysis of ovarian development. Results revealed that the biometrical parameters of wild and captive female broodstocks exhibited no remarkable difference (p > 0.05). Nevertheless, the wild fish had remarkably higher (p < 0.05) GSI (8.73%), oocyte weight (0.45 mg/egg), and ripeness (27.08%) in comparison with captive-reared broodstock. The total length and body weight, body weight and ovary weight, ovipositor diameter and ovary weight, and GSI and HSI displayed a positive relationship with R² = 1, R² = 1, R² = 0.993, and R² = 0.973, respectively, for wild broodstock, while R² = 0.994, R² = 0.806, R² = 0.804, and R² = 0.896, respectively, for captive broodstock. Additionally, the proximate composition in oocytes and liver tissues in both broodstocks did not differ significantly (p > 0.05). However, two essential amino acids (EAA), i.e., lysine and phenylalanine, and two non-essential amino acids, i.e., glutamic acid and glycine, were highly significant differences (p < 0.05) in the oocytes and liver of wild broodstock compared to the captive-reared broodstock. On the other hand, the EAA, e.g., isoleucine, threonine, leucine, and arginine, were highly dominated in both wild and captive female brood oocytes and liver. The ovarian histological slides from each fish group showed three oocytes developmental stages that indicated the asynchronous-reproductive ovarian oocytes of this fish. This study may be useful to fully understand the factors affecting the spawning and reproduction of S. aor broodstock, crucial for management in captive conditions as well as conservation and protection for sustainable aquaculture management of S. aor.