The melatonin hormone, which is a multifunctional molecule in vertebrates, has been shown to exert complex actions on the immune system of mammals. In teleosts, the immunomodulatory capacity of this hormone has seldom been investigated. In the present experiment, we exposed ex vivo spleen and head kidney tissues of pike-perch to melatonin (Mel) and cortisol (Cort). We applied three concentrations of both hormones, alone and in combination, namely (1) Mel (10, 100 or 1000 pg mL−1) (2) Cort (50, 500 or 5000 ng mL−1) (3) Mel + Cort (10 + 50, 100 + 500 or 1000 pg mL−1+5000 ng mL−1). Pure medium without Mel or Cort served as control. After 15 h of incubation, we assessed the expression of a set of immunity-related genes, including genes encoding for pro-inflammatory proteins (il-1β, cxcl8 and tnf-α), acute-phase proteins (fgl2, fth1, hepc, hp and saa1) and key factors of the adaptive immune system (fκbp4 and tcrg). Both Mel and Cort, when used alone or combined at physiological concentrations, significantly influenced immune gene expressions that may lead to a global immune stimulation. Our results support both, an indirect action of the Mel hormone on the immune system through the regulation of intermediates such as Cort, as well as a direct action on immune targets through specific receptors.