In May 2009, we studied the bivalve Spondylus crassisquama and its relevance for macrobenthic biodiversity off the north Ecuadorian coast. We found that the large and heavy shells offer an exclusive substrate for numerous epibiont species and highly specialized carbonate-drilling endobiont species (71 species in total), which is a distinctly different and much more diverse habitat than the surrounding sandy bottoms (13 species, 4 of them found in both habitats). This is reflected by a Bray–Curtis dissimilarity index of 0.88. We discuss in detail the live habits of all 9 species of drilling endobionts that we found, and conclude that these can be seen as true mutualists, with the exception of boring sipunculids and bivalves. To further illustrate this complex co-existence, we visualize and quantify for the first time the tremendous effects of boring organisms on the shell structure of S. crassisquama by means of magnetic resonance imaging and a video appendix is provided.