With coral cover and diversity declining on many coral reefs, a clearer understanding of large-scale reef dynamics is imperative. This paper presents a sampling program designed to quantify the sessile biotas of Caribbean reefs on large spatiotemperal scales. For each reef sampled, data are gathered along replicate, 25-m transects located within the habitat of interest. Herbivore impact is estimated by fish and echinoid censuses along the transects. High-resolution videotapes are used to estimate the percent cover of corals, algae, and other substratum occupants, and to estimate coral diversity. Finally, topographic complexity is measured along the transects. In at least some reef habitats, this index of three-dimensional structure provides a measure of the total disturbance regime, with flatter areas having been subjected to more intense, more frequent, and/or more recent sources of coral mortality. The techniques and statistical analyses described in this paper are simple, quick and inexpensive. Repeated sampling on multiple reefs will enable the investigator to detect changes in community structure and to test hypotheses of the causes of those changes.