Oil extracted from cloves, <em>Syzygium aromaticum</em>, consists mainly of eugenol, which has been documented to affect protozoa attachment, viability and growth. Isoeugenol (sold under the trade name AQUI-S<sup>®</sup>) is a commercially available fish anaesthetic produced by isomerisation of eugenol. Both are anaesthetics commonly employed during the husbandry and euthanasia of Atlantic salmon, <em>Salmo salar</em> L., used for amoebic gill disease (AGD) research. <em>Neoparamoeba perurans</em> (the causative agent of AGD) trophozoites were exposed to clove oil at 10, 20, 40 and 80 μL L<sup>−1</sup> for 10 min and 5, 10, 20 and 40 μL L<sup>−1</sup> for 120 min; AQUI-S<sup>®</sup> at 5, 10, 20 and 40 μL L<sup>−1</sup> for 10 min and 2.5, 5, 10 and 20 μL L<sup>−1</sup> for 120 min There were no significant differences in viability and survival of trophozoites after exposure to the anaesthetics. When trophozoites were exposed to clove oil at 80 μL L<sup>−1</sup> for 10 min there was significantly (<em>P</em> < 0.05) more detachment from a plastic surface compared to the control. Continued use of clove oil and AQUI-S<sup>®</sup> at 40 μL L<sup>−1</sup> or less for up to 120 min 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 <em>in vitro</em> screening of anti-<em>N. perurans</em> compounds.