Eight isonitrogenous (46% crude protein) and isolipidic (14% crude lipid) diets were formulated for juvenile black sea bass Centropristis striata to replace menhaden fish meal (FM) protein (59.5% CP) by three cottonseed meal (CSM) proteins: a CSM prepared from glandless seed (GCSM, 50.4% CP), a CSM that had been solvent extracted with acidic ethanol to remove the gossypol (SCSM, 53.8% CP), and a CSM prepared from regular (glanded) cottonseed (RCSM, 45% CP). Three diets replaced 50, 75 and 100% of FM protein with GCSM, and three diets replaced 50, 75 and 100% of FM protein with SCSM. One diet replaced 100% FM protein with RCSM protein. A control diet (0% CSM) was formulated with high FM protein and other practical protein sources. l-methionine and l-lysine were supplemented to the diets to equal the control diet. Fifteen fish were stocked in each of twenty-four 75-L tanks, and each test diet was fed to triplicate groups of fish (mean initial weight=7.7±0.10g) for 56days at 22–24°C, 32–35 salinity, and ambient photoperiod conditions. Fish were fed twice per day to apparent satiation. Final (day 56) mean body weight (BW, 24.16–31.62g), body weight gain (BWG, 211.2–311.3%), specific growth rate (SGR, 1.70–2.18%/d), and feed intake (FI, 0.37–0.43g/fish/d) were not significantly different (P>0.05) among the control, GCSM or SCSM treatments, but were reduced (P<0.05) for the 100% RCSM treatment (20.09g, 159.5%, 1.45%/d, and 0.25g/fish/d, respectively). Lower palatability of the RCSM diet was attributable to the anti-nutrient compound gossypol. No significant differences in survival (84.1–97.8%), feed conversion ratio (FCR, 1.05–1.33), protein efficiency ratio (PER, 1.62–2.08), or whole body protein or lipid composition were observed among the fish fed the low-gossypol diets. Gossypol (25.9mg/kg) was only detectable in the livers of fish fed the high-gossypol RCSM diet. Fish whole body essential amino acid compositions did not differ significantly among treatments. Whole body n − 3 PUFAs decreased, while n−6 PUFAs increased with increasing CSM protein in the diets. The apparent digestibility coefficient of protein was high (83.1–87.1%) for all treatments. For juvenile black sea bass, 75% FM in the diet can be replaced with low-gossypol CSM protein prepared by solvent-extraction, and 100% of FM can be replaced with low-gossypol CSM protein prepared from glandless seed with no adverse effects on survival, growth or feed utilization. Statement of relevanceCotton seed flour is an inexpensive agricultural by-product. The results demonstrate successful replacement of fish meal protein with genetically-improved cottonseed flour protein in the diet of black sea bass. These findings may substantially lower aquafeed costs (a key operational cost) for finfish growout operations to boost profitability and accelerate expansion of commercial production of black sea bass and other finfish species.