Context. Managing small, isolated populations requires conservation practitioners to weigh up the risks of inbreeding depression and outbreeding depression when assessing alternative management actions aimed at preventing species extinction. Accordingly, it is important that research intended to guide these management decisions provides the relevant evidence to inform them.

Aims. To determine the extent to which studies that use genetic analyses to characterise population units for conservation consider the key theoretical concepts necessary for making sound management recommendations regarding the desirability of gene flow among units, notably the consequences and relative risks of inbreeding depression and outbreeding depression.

Methods. A systematic search was conducted of peer-reviewed literature for studies that attempted to identify population units of threatened birds and mammals. Using content analysis, the theoretical framing of these studies was assessed, based on the discussion of key concepts concerning differences among populations.

Key results. There has been a significant increase over time in the number of published studies that use genetics to identify population units for conservation. Many do not consider theoretical concepts relevant to the effective management of fragmented populations of threatened species. Mammals were more common than birds as focal species of studies, but the number of concepts used in the framing of the studies was similar for these two taxa, despite differences in their ecology and biology that might be expected to affect perceptions of distinctiveness. Nevertheless, species of greater conservation concern tended to have a slightly more comprehensive theoretical framing.

Conclusions. There is great potential for more studies to implement theoretical guidelines and practical decision support tools when considering the best course of action for identifying appropriate population units for conservation management.

Implications. The gap in the identified literature is likely to be impacting the ability of conservation practitioners to make evidence-informed decisions about how to manage the genetic health of threatened species; it would be valuable to improve this situation.