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CORAL reefs are complex ecosystems threatened globally with a variety of natural and anthropogenic factors. Scientific monitoring is the primary source of information on reef biology and status. However, monitoring is both a scientific endeavor and a decisionmaking management tool. As a result, this dual nature leads to controversy and there is considerable debate among scientists about the design and methodology of these programs. Thus, although monitoring programs are often focused on important biological questions, they may have weak links to management and environmental policy. These links need to be strengthened for effective management and intervention.