The data for the manuscript "Effects of preservation by ethanol on δ13C and δ15N of three tissues of the critically endangered European eel Anguilla anguilla" are uploaded along with a readme file that explains the data column headings and information. The temporal effects of ethanol preservation on the δ13C and δ15N values of tissues excised from European eel Anguilla anguilla were assessed. Preservation significantly enriched 13C values of fin and mucus but not dorsal muscle. The 13C enrichment occurred in the initial 15 days of preservation and was independent of initial eel mass. Tissue preservation effects on δ15N values were negligible. These tissue-specific isotopic shifts should be considered when ethanol-preserved eel samples are used.