Anthropogenic chemicals in the aquatic environment are known to cause reproductive disturbances in vertebrate and invertebrate organisms by interfering with the endocrine systems. Large efforts have recently been devoted to dissect the mechanisms of action of xenobiotics in aquatic species, with the ultimate aim of detecting and controlling the effects of chemical exposure on the aquatic ecosystem and humans. In the present paper, males of a marine species, the black goby (Gobius niger), were treated with estrogenic and dioxin-like compounds commonly discharged into the environment from industry, agriculture, and urban waste such as nonylphenol (NP) and beta-naphthoflavone (beta-NF). Their effects were compared with those induced by estradiol (E2), analyzing the expression of biomarkers commonly used in ecotoxicological studies such as vitellogenin (VTG) and cytochrome P4501A1. The treatment with NP induced the synthesis of the female specific protein VTG in males, showing its estrogenic activity. NP and E2 lowered cytochrome P4501A1 basal levels while beta-NF determined a significant rise of its expression. The detoxification pathway was investigated, and the most relevant finding of this paper was the evidence that cytochrome P4501A1 inhibition by estrogen and estrogen-like compounds is mediated through the activation of the aryl hydrocarbon receptor repressor.