Restocking measures of the endangered European eel (Anguilla anguilla) have been set up in Europe since 2011. Restocking operations are performed with glass eel postlarval stage during their upstream migration. Restocking protocols involve the collection of glass eel in estuaries, transport and marking of 30% of the glass eels with Alizarin red S before restocking. All these restocking operations such as transport, handling, osmotic and thermal shock are a potential source of physiological stress for glass eels. The objective of the present study was to investigate the inter-individual responses to stress in the structure of the otoliths of restocked fish. This was achieved using otolith and experimental science. The originality of the present study was to address restocking stress for early stages of European eels. An experimental setting was performed by rearing glass eels obtained from a restocking program during 9 months. A control group was obtained by collecting wild glass eels at the entrance of a freshwater habitat. Relying on microstructure analysis of the sagittae otoliths and biometric measures, we aimed at investigating inter-individual variabilities of glass eels during their larval and glass eel stage and verifying the presence of additional stress marks related to restocking. The present results would be useful for improving eel restocking protocols or interrogating the relevance of restocking eels programs as a measure of recovery of healthy eel populations