Reef fish populations are conspicuous and essential components of coral reef ecosystems in the south Florida region. Recent precipitous declines in these populations are believed to be due to severe habitat degradation as well as significant increases in recreational and commercial fishing. The monitoring methodologies described in this document are necessary for understanding how natural and man-made stressors are changing reef fish populations and communities. These stressors will continue to increase, and understanding the responses of populations and communities will be critical for their sustainable management.