Indonesia is one of the countries in Asia region that plays an important role in the grouper supply. Grouper production in Indonesia increased 5-fold within two decades aside a continuous increase in grouper demand. To enhance grouper yield, the Indonesian Government initiated stock enhancement programmes releasing cultured grouper into the natural habitats. The purpose of the present study was to examine the impact of grouper stock enhancement onto natural grouper populations in Karimujawa National Park, Indonesia and to monitor the potential risks involved. Experimental release of 10 cm cultured Epinephelus fuscoguttatus (brown-marbled grouper) from the backyard multi-species hatchery system was monitored using underwater visual census and fish-catch monitoring. As a result, it was found that the greatest peril for the released grouper of 10 cm length was falling immediately prey to predators in the reef habitat, even though enough hides were available at the release site, since groupers of this particular size class were not trained to survive under field conditions. Grouper of 15 cm however are well capable of seeking shelter and avoiding predators. This leads to the clear recommendation that released grouper should to have a size of at least 15 cm for release in stock enhancement programmes. According to our experiments the so far officially recommended minimum size of release (10 cm) is therefore too low and should be increased to 15 cm for E. fuscoguttatus, and requires future adjustment of the official recommendations in use. Parasitological examination of the released fish was conducted in order to analyse potential risks involved. No macro-parasites could be observed, limiting the risk of spreading parasites and diseases within the Indonesian archipelago. However, many parasites of E. fuscoguttatus are widespread and can infect different grouper species.