To determine the pathogenicity of Acanthamoeba spp. isolated in Korea and to develop a isoenzymatic maker, the mortality rate of infected mice, in vitro cytotoxicity against target cells and isoenzyme band pattern were observed. Five isolates of Acanthamoeba spp. (YM-2, YM-3, YM-4, YM-5 and YM-7) were used in this study as well as three reference Acanthamoeba spp. (A. culbertsoni, A. hatchetti, and A. royreba). According to the mortality rate of infected mice, Korean isolated could be categorized into three groups: high virulent (YM-4), low virulent (YM-2, YM-5, YM-7) and the nonpathogenic group (YM-4), In addition, the virulence of Acanthamoeba spp. was enhanced by brain passage in mice. In the cytotoxicity assay against chinese hamster ovary cells, especially, the cytotoxicity of brain-passaged amoebae was relatively higher than the long-term cultivated ones. The zymodeme patterns of glucose-6-phosphate dehydrogenase (G6PD), malate dehydrogenase (MDH), hexokinase (HK), glutamate oxaloacetate transaminase (GOT) and malic enzyme (ME)of Acanthamoeba spp. were different among each isolate, and also between long-term cultrued amoebae and brain passaged ones. In spites of the polymorphic zymodemes, a slow band of G6PD and K, and an intermediate band of MDH were only observed in pathogenic Acanthamoeba spp., which should be used as isoenzymatic makers.