Acanthamoeba species are ubiquitous in natural and man-made environments worldwide; some strains are able to colonize human eyes as facultative parasites. It has been shown that environmental and clinical isolates/species of Acanthamoeba vary in their pathogenicity. In this study we examine and compare the in vitro effects of the changing temperature on the population dynamics of subsequent amoebic strains. Identification of Acanthamoeba strain by morphological and molecular methods and temperature assays were performed. Monitoring of the corneal and environmental strains showed changes in population densities and a termo-tolerance correlating with pathogenicity of amoebae. Comparative assessment of results indicated differences in viability of amoebic populations in exponential growth phase in vitro cultivation. The increased awareness of the threat is needed for better understanding of impact of factors examined on pathogenesis in human infected with Acanthamoeba strains.