The domestication process is accompanied by adaptation of the animals to captive conditions. It induces changes at different levels thereby affecting a variety of biological functions. While there is abundant literature on the domestication effects on growth and stress response in teleosts, the effects on reproduction have received limited attention. In this work, we investigated the domestication effect on the reproductive ability of Eurasian perch (Perca fluviatilis L.), a promising candidate for the development of European aquaculture and whose reproductive physiological processes through the domestication history have not been questioned yet. To address this question, two populations of F1 and “domesticated” females were subjected to a photothermal program allowing the control of gonadogenesis advancement. Gonadosomatic index, 17β-Estradiol levels, and oocyte diameter were significantly higher in the “domesticated” population than in F1 population. In contrast, testosterone, 11-ketotestosterone, and vitellogenin levels were found to be higher in F1 females than in their “domesticated” counterparts. Lower reproductive performance was observed in the “domesticated” population compared to the F1 population in terms of embryo survival, percentage of eyed-stage larvae, hatching and percentage of malformation rates. In conclusion, this study shows that despite a positive effect on advancing gonadogenesis and vitellogenesis, this domestication route negatively affected the reproductive performance under our conditions. Statement of relevance This work will give information to producers to choose good broodstock populations (wild or domesticated) to have optimal reproductive performances in Eurasian perch, and thus improve fish production.