This method for separating coral tissues from algal endosymbiont (Symbiodiniaceae) for stable isotope analysis is modified from previously published methods (Hughes et al. 2010). There are three parts to preparing coral samples for stable carbon and nitrogen isotope analysis: 1) airbrush to remove coral tissue and algal cells from skeleton and store at -80 °C until ready to separate, 2) separate the coral tissue from the algal cells through centrifugation and filtering, and 3) dry and pack separated tissues into tin capsules for analysis in a stable isotope ratio mass spectrometer. This method was modified from Hughes et al. (2010) by James Price with the assistance of Alex Smith and Kerri Dobson and with the guidance of Andréa Grottoli at The Ohio State University. dx.doi.org/10.17504/protocols.io.bgi7juhn