Stable isotope analyses are widely used to determine trophic levels in ecological studies. We have investigated the effects of carbonate removal via acidification on the stable carbon and nitrogen isotopic composition of 33 species of tropical benthic macrofauna, and we report guidelines for standardizing this procedure for higher taxa in tropical coral reef ecosystems. Many tropical benthic invertebrates are small in size, and therefore body tissue isolation (separating organic carbon from inorganic structures) is difficult and time-consuming. Literature reviews of invertebrate studies show a lack of consistent procedures and guidelines for preparation techniques, especially for carbonate removal via acidification of whole individuals. We find that acidification decreases the delta C-13 values of samples containing carbonate, with shifts ranging from 0.21. to 3.20 parts per thousand, which can be related to CaCO3 content (assessed by a carbonate proxy), justifying acid pre-treatment. Carbonate-containing taxa benefiting; from acidification included Amphinomida, Terebellida (Annelida), Anomura, Brachyura, Caridea, Amphipoda, Tanaidacea (Arthropoda) and Edwardsiida (Cnidaria). The delta C-13 Shifts Of samples containing no carbonate varied tip to 0.02 +/- 0.20 parts per thousand. As this induced delta C-13 shift was lower than the range of an average trophic level shift (0.5 to 1 parts per thousand), we conclude that acid pre-treatment is unnecessary. Carbonate-free taxa consisted of Eunicida, Phyllodocida (Annelida) and Mollusca. We note minimal impact of acidification on delta N-15 values except for Brachyura, which showed a shift of 0.83 +/- 0.46 parts per thousand, which is still lower than a single trophic level shift (2.9-3.8 parts per thousand). We conclude that for trophic level studies, both the delta C-13 and the delta N-15 of carbonate-rich macrofauna can be determined from the same acidified sample. Copyright (C) 2008 John Wiley & Sons, Ltd.