Wheat rust can cause catastrophic crop failures. The Green Revolution succeeded in part thanks to the deployment of wheat with genetic resistance to stem rust. The appearance of a new strain of stem rust in Uganda (Ug99), first detected in 1998, raised the threat of global stem rust epidemics beyond its prevalence in Africa and the Middle East. Despite over twenty years of awareness campaigns, research, and breeding programmes, much of the wheat cultivated today still lacks resistance to Ug99, while races of the stripe and leaf rust present equal challenges to meeting market demands. Our article contributes a new assessment of ethical issues that emerge in our fight against stem rust. Specifically, the article explores how efforts to combat stem rust we employ today may threaten genetic diversity in wheat or impose a further bottleneck on choice of cultivars, thus directly impacting the ability of future generations to fight stem rust and also to find the genetic diversity needed to develop new varieties of wheat that are adapted to changes in climate.