Benthic census data were collected from sites around Micronesia as part of the ongoing Micronesia Challenge. Information on the program can be found at (www.micronesiareefmonitoring.com). Survey sites were selected around each island to be representative of natural environmental gradients, management, and major reef types. Thus, full site designs can be used to evaluate both island trends and site-specific trends. Benthic substrates were evaluated using a photo-quadrat technique. At each site, five 50-m transects were used to measure fishes, corals, and other benthic assemblages between 8–10 m on outer reefs, and at 3–5 m for inner lagoon reefs.Fifty photos were taken at 1-m intervals along each 50-m transect line. Within each photo the benthic substrates were evaluated under five randomly allocated crosses. Benthic-assemblage metrics were derived from data aggregated across the 50 photographs, to the transect level (n = 5). Metrics included coral and macroalgal cover, coral-genus richness, and a benthic substrate ratio defined by the percentage cover of heavily calcifying (corals and CCA) versus non-or-low calcifying (turf, encrusting, and macroalgae) substrates.