A 35-d growth trial was conducted to evaluate the effect of fertilization with flaxseed meal versus cottonseed meal on fingerling red drum (Sciaenops ocellatus) production characteristics (individual weight, total length, and percent survival), water quality parameters, and zooplankton densities in plastic-lined ponds. Red drum fry were stocked into 16 randomly allocated 0.40-ha ponds, with eight ponds per fertilization treatment. Mean individual weight of red drum fingerlings was significantly larger in ponds fertilized with flaxseed meal than in ponds fertilized with cottonseed meal throughout the growth trial. Similarly, red drum fingerlings had significantly greater mean length in ponds fertilized with flaxseed meal during the first 25 days of culture; however, no difference in total length was observed at the termination of the growth trial. No differences were observed for water quality parameters between treatments except for pH, which was significantly higher in ponds fertilized with cottonseed meal. Rotifer populations were significantly greater in ponds fertilized with CSM than FSM; however, no differences in total copepods, total copepod nauplii, or total zooplankton densities were observed between pond treatments. Our results indicated the growth of red drum fingerlings was enhanced in ponds fertilized with flaxseed meal. Furthermore, at the rate used in this study (392 kg/ha), flaxseed meal did not negatively impact water quality or zooplankton populations in fingerling red drum production ponds. However, initial cost-benefit analysis suggests that utilizing flaxseed meal for red drum production is cost prohibitive compared to cottonseed meal. Further research is needed to determine specific impacts of the flaxseed meal application to marine ponds as well as the economic feasibility of adding flaxseed meal to production ponds before this procedure can be recommended for red drum fingerling production.