The Structured Analysis Methodology (SAM) is an application of the systems ecology paradigm (SEP). SAM was built as a “tutorial” to guide community-based, collaborative stakeholder groups through analysis and resolution (decision-making) of complicated and complex natural resource, environmental, and societal challenges. Stakeholders are scientists, managers, policy decision-makers, and citizen leaders. SAM was initially created to address landscape- to regional-scale ecosystem management challenges, but it can be applied to many other complex problems. During the problem analysis phase of SAM several critical steps must be accomplished (e.g., SAM requires precise, transparent, and agreed-upon statements of problems and goals; detailed descriptions of associated space, time, and institutional dimensions of the problem must be made; SAM demands inclusion of important stakeholders; and as the problem analysis develops, the stakeholder group initiates and refines conceptual models of how the defined ecosystem functions and behaves). Conceptual models often require systems or simulation modeling for further analysis and clarification. Following the analysis phase, the stakeholder group develops management options (e.g., ecosystem management), chooses among them (decision-making), and implements one or more. The implemented plans must be monitored and if they are not working make adaptations. Adaptation may require reiteration of part or all of the SAM.