Neoparamoeba pemaquidensis believed to be the most prevalent parasite of Atlantic salmon industry in Australia. In the present study, the in vitro effects of crude extract of garlic and metronidazole were investigated using a primary culture toxicity assay. Garlic extract appeared to be completely effective at killing a cultured strain (NP251002) of Neoparamoeba pemaquidensis in vitro at a dilution of 1:100 with in 24 h. The number of viable Amoebae after using garlic extract in lower dilutions (1:200, 1:400, 1:800, 1:1000) for 24 h, also were significantly lower than in the control group. Garlic extract was also efficacious at killing wild type Amoebae that isolated from the diseased fish showing clinical signs of AGD. Metronidazole had no clear effect against Neoparamoeba pemaquidensis (NP251002) even in a concentration of 50 mg L(-1) for 24 h. However some morphological changes have occurred in metronidazole-treated Amoebae after 5 days of exposure.