Different kinds of experimental calcareous substrates were exposed at Lee Stocking Island (Bahamas) and One Tree Island (Great Barrier Reef, Australia) to study which endolithic bacteria, algae and fungi contribute to bioerosion and what their bioerosion rates are. The sites at Lee Stocking Island were several leeward shallow water and several windward shallow and deep-water positions (from the Acropora palmata reef at 2 m down to 275 m depth). At One Tree Island, the experiments were conducted in patch reefs treated with P and N to study the influence of mineral nutrients on bioerosion. The exposure periods ranged from 1 week to 2 years. The micritic carbonate substrates exposed on Lee Stocking Island contained 6 genera with 15 species of cyanobacteria, green and red algae, and different kinds of microendolithic heterotrophs. The mean values of bioerosion rates measured between 1 to 2 g/m 2 /y at 275 m and 520 g/m 2 /y at one of the leeward sites. The composition of the endolithic community and the bioerosion rates changed over time. At One Tree Island, shell pieces of Tridacna were used as substrate exposed for 5 months to endolith activity. Five genera and 6 species of cyanobacteria, green and red algae and different kinds of heterotrophic microendoliths were found with bioerosion rates of 20–30 g/m 2 /y. There are differences in abundance of taxa between Lee Stocking Island and One Tree Island. The introduction of nutrients had no apparent impact on the microborer community. Controlling factors for the distribution and abundance of microborers are mainly light, but also the kind of substrate and, possibly, the biogeographic position. The results support the paleoecological importance of microendoliths.