This is the first quantitative study on the prevalence of epizoic Waminoa sp. acoel worms and their association with corals in the Wakatobi Marine National Park (WMNP), South-East Sulawesi, Indonesia. Three replicate transects were laid on the reef crest, flat and slope at six sites in 2006 and eight sites in 2007. Four of the sites were common in both years. In total 69 transects were surveyed in 2006, and 87 transects in 2007. A total of 4.8% of all observed hard corals were associated with acoel worms in 2006 and 2.6% of hard and soft corals in 2007. Acoels were present on 16 and 21 of the coral taxa studied in 2006 and 2007 respectively. The worms were strongly associated with the azooxanthellate coral Tubastrea spp. and were rare or absent on the most abundant coral genera Montipora and Porites. The mean number of corals having acoels was highest on reef slopes, whereas acoels were virtually absent on reef flats. Corals that had a high and a medium cover of worms were more common in 2007 than in 2006. No significant trend in the adaptation of the zooxanthellae of Waminoa sp. to different depths at different sites was revealed. The impact of the worm on the coral is unknown, but high numbers may have a shading effect and a negative impact on the coral's photophysiology. This acoel merits more study of its life cycle, its photophysiology, and its impact on its host corals.