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Anaesthetics are widely used in aquaculture, fisheries, and biological research as a method to minimize fish stress and injury during handling and transport. Considerations such as efficacy, cost and environmental effect as well as its toxicity to fish are evaluated to choose a suitable anaesthetic. In the same way, several fish anaesthetic agents have been reported in fish including their safe dosage; however, scarce information is available about gene expression under anaesthetic stages. In this work, gene expression of hypoxia‐inducible factor 1 alpha (HIF1a) and the glucocorticoid receptor (GlucoR) was assessed as indicators of stress in the Colombian native fish species red‐bellied pacu (Piaractus brachypomus) under anaesthesia with menthol (50 mg/L) and eugenol (40 mg/L). Results of this study indicated that the exposure of red‐bellied pacu fingerlings to effective concentrations of the menthol generated a differential gene expression of HIF1a mRNA that was significantly higher in the liver for menthol group, and in the case of GlucoR mRNA, it was significantly higher in gills and blood of fish under eugenol anaesthesia. This is the first report of gene expression in this native fish species. [ABSTRACT FROM AUTHOR]