We review critical issues that must be considered when selecting indicator species for a monitoring program that aims to maintain or restore ecological integrity. First, we examine the pros and cons of different management approaches on which a conservation program can be based and conclude that ecosystem management is most appropriate. We then identify potential indicators of ecological integrity at various levels of the ecosystem, with a particular emphasis on the species level. We conclude that, although the use of indicator species remains contentious, it can be useful if (1) many species representing various taxa and life histories are included in the monitoring program, (2) their selection is primarily based on a sound quantitative database from the focal region, and (3) caution is applied when interpreting their population trends to distinguish actual signals from variations that may be unrelated to the deterioration of ecological integrity. Finally, we present and discuss different methods that have been used to select indicator species.