Hybridisation and introgression affect a range of species globally, challenging the biological species concept. Animals that blur our definitions complicate species management as there are limited policies and guidelines to shape our decisions for dealing with such animals. This is particularly important for threatened species affected by hybridisation by either wild species or their domesticated relatives, where, especially for the latter, management may result in lethal control of hybrid animals. We investigate the degree of threat by hybridisation to threatened vertebrates globally, by analysing the key threats for species listed on the IUCN Red List. We then analyse mammalian species threatened by hybridisation in particular, to identify to what extent policies have been developed to address the issue. Using case studies, we discuss how lack of appropriate policies can lead to inaction in conservation management, and where human-wildlife conflict occurs, ambiguity allows affected stakeholders to interpret policy to suit their purpose, such as livestock producers culling wild canid-dog hybrids. We argue that research is needed to determine the biological role of hybrids which should inform policy on a species-by-species basis.