A wide range of animal taxa, including vertebrates and invertebrates, are controlled or kept by humans. They may be used as pets, for recreation, sport and hobbies, as working animals, as producers of animal-derived (food) products or as biomedical models in research. There is a need for clear guidance on the treatment of animals, regardless of their phylogenetic distance from humans. Current animal welfare concepts, which emphasise animal sentience and the ability of animals to experience negative or positive mental states, are limited in scope to a small proportion of the animal kingdom, as the vast majority of species are (currently) thought to lack sentience. We discuss four options for addressing the question of which basic concept(s) could be used to derive guidelines for the treatment of animal species, sentient or non-sentient: (1) alternative concepts tailored to specific groups of species; (2) ‘welfare’ concepts not presupposing sentience; (3) the precautionary principle; or (4) the concept of animal integrity. Since questions regarding the appropriate treatment of animals, including species with a large phylogenetic distance from humans, have an ethical/moral dimension, we also address who counts morally and how much, and how animals should be treated given their moral status. We suggest that the concept of animal integrity, possibly complemented and extended by the concept of habitat/ecosystem integrity, is suitable for application to all species. However, a current concept of animal welfare should serve as the primary basis for guidance on how to treat species that are sentient and capable of experiencing emotions.