Microalgal-based indicators were used to assess terrestrial influence on Shiraho coral reef of Ishigaki Island (Okinawa, Japan). A typhoon occurred on 4-5 August 2005 and sampling were made on three occasions thereafter (6, 8, and 11 August). Pre-typhoon sampling was conducted on 26 July. The typhoon-enhanced terrestrial discharges increased reef nutrient levels (e.g. average NO(3)(-)-N: 0.088mg/L pre-typhoon to 0.817mg/L post-typhoon). This elevated chlorophyll-a concentrations by four times and shifted phytoplankton composition (spectral class-based) from an initial dominance of diatoms and green microalgae to the dominance of bluegreen microalgae (cyanobacteria) and cryptophytes. Cyanobacteria later increased by more than 200% and accounted for as much as 80% of total chl-a ( approximately 0.29microg/L), possibly assisted by favorable nutrient availability. In outer reef waters, diatoms and green microalgae predominated whereas cyanobacteria and cryptophytes were nearly undetectable. Due to detrital decomposition and river discharge, the CDOM was much higher in the inner reef than in the outer reef. Benthic bluegreen microalgae were relatively more abundant in areas close to the river mouth and coastal agricultural fields. At these locations, nutrient concentrations were much higher due to river discharge and potentially significant groundwater discharge. Thus, phytoplankton and benthic microalgae can serve as indicators of terrestrial influence on coral reefs.