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More than 1,500 species of plants and animals in the United States are listed as threatened or endangered under the Endangered Species Act and habitat destruction is the leading cause of population decline. However, developing conservation plans that are consistent with a diversity of stakeholder (e.g., states, tribes, private landowners) values is difficult. Adaptive management and structured decision-making are frameworks that resource managers can use to integrate diverse and conflicting stakeholder value systems into species recovery planning. Within this framework difficult decisions are deconstructed into the three basic components: explicit, quantifiable objectives that represent stakeholder values; mathematical models used to predict the effect of management decisions on the outcome of objectives; and management alternatives or actions. We use Bull Trout Salvelinus confluentus, a species listed in 1999 as threatened pursuant to the Endangered Species Act, as an example of how structured decision-making transparently incorporates stakeholder values and biological information into conservation planning and the decision process. Three moral philosophies-consequentialism, deontology, and virtue theory-suggest that structured decision-making is a justified method that can guide natural resource decisions in the future, consistent with United States Congress' mandate, and will honor society's obligation to recover Endangered Species Act listed species and their habitats. Natural sciences offer a biological basis for predicting the outcomes of decisions. Additionally, an understanding of how to integrate humanities into scientifically defensible conservation planning is helpful in providing the foundation for lasting and effective species conservation.