The domestication of fish species is still in its early stages when compared to terrestrial animals. The effects of domestication on welfare of farmed fishes are complex because fish differ from livestock in genetics, physiology and behaviour, and experience different sensory worlds. Consequently, empathy with fish and understanding of their needs becomes more problematic than with land animals. Additionally, the acknowledgement and study of mental dimensions of fish existence is very recent. We discuss that higher levels of domestication in fish do not necessarily correspond to better welfare because 1) artificial selection by the aquaculture industry is mostly focused on production-related traits such as growth, and this selection process may have unknown negative effects on welfare-related traits, 2) the number of fish species presently farmed (circa 300) is tenfold higher than land animals, rendering the establishment of standard welfare guidelines extremely complicated, 3) the current paradigm of the Five Freedoms guiding welfare is out-dated and was designed for livestock and 4) there are still severe knowledge gaps in the biology of farmed fishes, especially in welfare-related traits. The implementation of humane farming systems should integrate industry, science and ethics in an open dialogue in order to produce relevant results.