Abstract Ecotoxicological studies aim to assess the potential environmental risks of various products. This implies the use of various biological models and tests on live animals. In case of handling fish and mammals, ethical rules have to be respected. The use of anaesthesia is considered to be the best way to ensure animal welfare. Eugenol and electro-narcosis are among the most popular chemical and physical anaesthetics used in fisheries and by field biologists. In this study, the genetic and endocrine impacts of these anaesthetics were assessed in order to establish whether the use of such methods could skew the results of ecotoxicological studies. Twenty yellow European eels ( Anguilla anguilla) were submitted to Eugenol (50 mg/L) and electro-narcosis until they reached a level of deep anaesthesia, while 20 other eels were kept aware. Five anaesthetized and five unanaesthetized eels were sacrificed and analysed directly after treatment and after 1, 7 and 21 days of recovery. At the brain level, Eugenol triggered an increase in the transcription level of genes encoding proteins involved in oxidative stress responses (catalase expression 2.5-fold, mitochondrial superoxide dismutase expression 3-fold), probably due to a hypoxic event during anaesthesia. Later impacts were detected in muscles 21 days after anaesthesia (ATP synthase subunit 6 3-fold, NADH deshydrogenase subunit 5 4-fold and mitochondrial superoxide dismutase 3-fold increased) revealing oxidative stress from an accrued mitochondrial respiratory metabolism. Hormone dosages showed that the use of Eugenol reduced the release of plasma cortisol during anaesthesia. However, this impact seemed to be reversible within one day. In case of electro-narcosis, no significant variation in transcriptional levels could be detected between anaesthetized and unanaesthetized eels. Our results suggest that the use of Eugenol as an aesthetic in ecotoxicological studies measuring gene expression or plasma cortisol concentration is not appropriate, while electro-narcosis does not seem to have any impact, at least on the parameters taken into consideration in this study.