The deep sea, especially hadal zones, characterized by high-hydrostatic pressure, low temperatures, and near-total darkness, present some of the most challenging environments for life on Earth. However, teleost fish have successfully colonized these extreme habitats through complex adaptations. We generated genome assemblies of 12 species, including 11 deep-sea fishes. Our findings reconstructed the teleost deep-sea colonization history and revealed the overall impact of the deep-sea environment on fishes. Interestingly, our results question the previously assumed linear correlation between trimethylamine oxide (TMAO) content and depth. By contrast, we observed a convergent aa replacement in the rtf1 gene in most deep-sea fishes under 3,000 m, and in vitro experiments suggest that this mutation can influence transcriptional efficiency, which is likely to be advantageous in the deep-sea environment. Moreover, our study underlines the pervasive impact of human activities, as we detected the presence of persistent organic pollutants in species from the Mariana Trench.