The purpose of this study was to determine whether gilthead sea bream and sea bass treated with combination of trimethoprim and sulfamethoxazole (TMP-SMX) differed in terms of physiological and innate immune biomarkers. Fish were exposed to TMP-SMX at 40 ppm concentration for 1 h as a prophylactic usage. Plasma cortisol, glucose, electrolytes (Ca, P, Na, K, Cl, and Mg) as well as plasma lysozyme activity, C-reactive protein (CRP), and ceruloplasmin (Cp) were measured soon after treatment and following 24 and 48 h in normal sea water for recovery. Treatment with TMP-SMX in both gilthead sea bream and sea bass led to an increase in plasma cortisol and glucose. Fluctuations in some electrolytes were found after treatment and during recovery period, however, the ratios of monovalent ions in treated sea bream were similar to control. Hematocrit values as well as plasma lysozyme activity in gilthead sea bream and sea bass were not affected by the treatment. CRP in gilthead sea bream and Cp in sea bass responded to the treatment with decreased levels. Both gilthead sea bream and sea bass displayed a rapid physiological stress response and sensitivity to TMP-SMX exposure, which requires more than 48-h period for regaining homeostasis.