Genetic rescue is a measure to mitigate the effects of reduced genetic variation in endangered small, isolated (inbreed) populations by introducing new genetic variation into such populations. This is usually accomplished by translocating individuals from a related population, assumed to belong to the same, often polytypic species, into the endangered population. If, however, the taxonomic classification does not reflect the ‘true’ diversity, genetic rescue can have detrimental effects on the survival of the endangered population (e.g. outbreeding depression). Here we point to problems if erroneous taxonomy informs such translocating strategies. Actions that promote artificial admixture of evolutionary lineages may be ineffective, or they may homogenize existing diversity and biogeographic patterns instead of protecting them. The extreme result is to drive target species and/or cryptic lineages to silent extinction. We single out conspicuous examples to illustrate the negative impacts of actions, which have resulted from artificial interbreeding of evolutionary distinct species or ill-conceived ‘genetic augmentation’. In such cases, translocations negate the overarching objective of biodiversity conservation: embodied in the concept of phylogenetic distinctiveness (PD), the encompassing scientific foundation of biodiversity conservation aims to maximize representation of the evolutionary history at the levels of species and ecosystems. A major underlying problem that we identify is persisting taxonomic inertia maintaining e.g., an overly simplified ungulate taxonomy, which is in most cases equivalent to a certain genomic incompatibility or a dilution of specific adaptations. Translocations and genetic rescue should only be employed, if potentially negative effects of the measures can be ruled out (including wrong taxonomy). Poor taxonomy has been – and indeed remains – at fault.