The aim of 2TEM was to develop a non-lethal method to determine the salinity habitat of eel. The European eel spawns in the Sargasso Sea but grows in Europe and North Africa. Most eels grow in freshwater, but others settle in marine coastal habitats. Some shift between freshwater and seawater during their growth phase. The salinity habitat of eels is currently determined by sacrificing eels and analyzing their otoliths (ear stones). We hypothesized that their salinity habitat could be predicted by sampling their blood. We tested this on 60 eels from different habitats and compared the results of blood and otolith analyses: 39% were seawater residents, 43% habitat shifters and 18% freshwater residents. Eels were almost all correctly classified (93%) based on the blood transcriptomes, providing a reliable non-lethal method to determine the salinity habitat of the endangered European eel.