Flagship species are those chosen to raise support for broader conservation marketing campaigns and can be used as symbols of the ecosystem services and evolutionary history of particular areas. Thus, flagship species can be employed for the protection of endangered species and threatened ecosystems. Northeastern Michoacán, Mexico, is an important region for amphibian diversity but approximately 40% of its mature forest has been removed. Among northeastern Michoacán amphibians, the use of Ambystoma ordinarium as a flagship species is supported by its co-occurrence with other threatened amphibians along riparian zones. To support this proposal, however, it is important to assess the functional traits and evolutionary history of amphibian species sharing their habitat with A. ordinarium. To evaluate the potential of A. ordinarium as a flagship species, we estimated the functional and phylogenetic diversity of amphibian assemblages in 60 riparian zones. The results showed that amphibian assemblages sharing habitat with A. ordinarium presented higher functional and phylogenetic diversity than those in which this species was absent. These results highlight the potential of A. ordinarium as a flagship species for the protection of associated amphibian species, their functions, and evolutionary history.