RATIONALE Stable isotope analysis has been used extensively to provide ecological information about diet and foraging location of many species. The difference in isotopic composition between animal tissue and its diet, or the diet‐tissue discrimination factor, varies with tissue type. Therefore, direct comparisons between isotopic values of tissues are inaccurate without an appropriate conversion factor. We focus on the loggerhead sea turtle ( Caretta caretta ), for which a variety of tissues have been used to examine diet, habitat use, and migratory origin through stable isotope analysis. We calculated tissue‐to‐tissue conversions between two commonly sampled tissues. METHODS Epidermis and scute (the keratin covering on the carapace) were sampled from 33 adult loggerheads nesting at two beaches in Florida (Casey Key and Canaveral National Seashore). Carbon and nitrogen stable isotope ratios were measured in the epidermis and the youngest portion of the scute tissue, which reflect the isotopic composition of the diet and habitat over similar time periods of the order of several months. RESULTS Significant linear relationships were observed between the δ 13 C and δ 15 N values of these two tissues, indicating they can be converted reliably. CONCLUSIONS Whereas both epidermis and scute samples are commonly sampled from nesting sea turtles to study trophic ecology and habitat use, the data from these studies have not been comparable without reliable tissue‐to‐tissue conversions. The equations provided here allow isotopic datasets using the two tissues to be combined in previously published and subsequent studies of sea turtle foraging ecology and migratory movement. In addition, we recommend that future isotopic comparisons between tissues of any organism utilize linear regressions to calculate tissue‐to‐tissue conversions. Copyright © 2014 John Wiley & Sons, Ltd.