Natural environments are now much reduced or modified, with the consequence that many species have declined and become imperilled. However, such modifications have also led to range expansion or population increases in some other native species. Consequently, in an increasing number of situations, the viability of a threatened native species is now being compromised by another native species, and conservation managers must consider options for how best to make decisions about and manage such situations. Here, I provide Australian examples of the many variations of the issue of managing to favour one native species at the expense of another native species, and note that the issue is likely to be of increasing incidence, extent, complexity and societal interest. Whereas there are reasonably well-established policy and legal foundations, and general societal support, for killing invasive (‘pest’ or ‘weed’) species to benefit native species, there is far less well-developed context and regulatory basis for the issue of killing native species to benefit other native species, and it may evoke considerable community concerns. Given the moral complexities of this issue, I use and apply the long-established ‘Just War’ theory as a pathway to develop a simple decision tree approach and a set of principles to guide decision-making when considering the need to kill a native species to achieve a conservation objective. These principles are that: (i) every effort should first be made to redress any ultimate factor responsible for the ecological imbalance; (ii) there should be compelling evidence that the ‘increaser’ species (‘Species A’) has a significant detrimental impact on the species of conservation concern (‘Species B’); (iii) there should be compelling evidence that reduction in the abundance of Species A will lead to a significant and enduring enhancement of the conservation outlook for Species B; (iv) reduction in the abundance of Species A will have no significant impact on its conservation status; (v) consequently, any program of killing Species A should be predicated on a net biodiversity benefit; (vi) options other than killing have been adequately evaluated as a mechanism to reduce the impact of Species A on Species B; (vii) any killing of Species A is done as humanely as possible; (viii) all relevant information on the situation is provided publicly with opportunity for public comment prior to decision-making; (ix) where there is insufficient information about any proposed culling, a carefully-designed trial should be applied, with results used to guide subsequent decision-making; (x) the management actions and biodiversity responses are monitored and reported publicly.