Invertebrate 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. Each 50-m transect was surveyed at a 5-m width by either one or two observers. Invertebrates were identified to the lowest possible taxon and enumerated. When possible, a size esitmate to the nearest 5 cm was provided.