Oil extracted from cloves, Syzygium aromaticum, consists mainly of eugenol, which has been documented to affect protozoa attachment, viability and growth. Isoeugenol (sold under the trade name AQUI-S«) is a commercially available fish anaesthetic produced by isomerisation of eugenol. Both are anaesthetics commonly employed during the husbandry and euthanasia of Atlantic salmon, Salmo salar L., used for amoebic gill disease (AGD) research. Neoparamoeba perurans (the causative agent of AGD) trophozoites were exposed to clove oil at 10, 20, 40 and 80áμLáL−1 for 10ámin and 5, 10, 20 and 40áμLáL−1 for 120ámin; AQUI-S« at 5, 10, 20 and 40áμLáL−1 for 10ámin and 2.5, 5, 10 and 20áμLáL−1 for 120ámin There were no significant differences in viability and survival of trophozoites after exposure to the anaesthetics. When trophozoites were exposed to clove oil at 80áμLáL−1 for 10ámin there was significantly (Pá<á0.05) more detachment from a plastic surface compared to the control. Continued use of clove oil and AQUI-S« at 40áμLáL−1 or less for up to 120ámin is unlikely to have a detrimental impact on amoebae that are isolated and collected from salmon with AGD to be used for downstream research such as projects involving disease challenges and in vitro screening of anti-N. perurans compounds.