Of all the steps in monitoring, choosing the correct indicators is arguably the most important. The challenge is obvious: among all the possible attributes of an ecosystem that can be measured, select a small number whose measurement will tell you something about all of the unmeasured attributes and processes. Even if a monitoring program is fully funded and implemented for many years, it will fail if the wrong indicators were selected. Yet establishing a strong logical basis for indicator selection is often overlooked. It is not unusual to discover that great thought and deliberation have gone into how, when, and where to measure a given indicator, but little discussion of why that particular attribute is being measured, what magnitude of change needs to be detected, and what the indicator tells you about unmeasured components of the ecosystem. Further adding to the challenge is the fact that there is no prior reason to expect agreement between scientists, managers, and the public on those attributes of ecological systems most logical and important to measure. How can one narrow down the field of all possible attributes and reach agreement on what to measure? Unfortunately, science provides limited guidance because no body of ecological theory or empiricism exists to precisely guide indicator selection. We therefore contend that partnerships are critically important to the development of prior agreements between multiple parties. Critical to this process is the collaborative development of common paradigms concerning how ecosystems are conceptualized. We believe this is best accomplished if scientists and managers collaborate in the following steps: 1) develop a conceptual model which reflects the hierarchial structure of the ecological system to be managed; 2) view the environmental hierarchy as a set of filters which constrain the plant and animal species observed on the ground; 3) identify the collection of traits of a set of focal species that reflect the desired states of the environmental filters; 4) focus on the factors that adversely affect the state of the environmental filters (in other words, take a stressor-based approach to monitoring). These steps should lead to a logical group of focal species and stressors to be monitored.