A biological survey of the South Moloka’i coral reef was undertaken by the University of Hawai’i Coral Reef Assessment and Monitoring Program (CRAMP) in support of the extensive effort by USGS to characterize sediment dynamics on the south Moloka’i reef flat. The experimental design and sampling sites for the USGS project were established primarily to document patterns of sediment input, distribution and sediment output on the south Moloka’i reef in the area between Kamalo and Kaunakakai. The overall project experimental design was not driven by biological questions, but rather was designed to establish baseline data for water quality data and sediment distribution. The focus of the biological support component was to describe the biological condition at each of the USGS sediment/water quality sampling sites. The biological data were taken in a manner that will enable a future quantitative evaluation of possible changes in the benthos at each site over time. These data can then be related to any changes in turbidity, suspended sediment concentrations, or sediment on the reef flat.