This study was conducted to address the distribution of Acanthamoeba genotypes in therapeutic hot springs in Iran. Sixty water and sediment samples were collected from bicarbonate, sulphur, and sodium chloride thermal springs in the northwest. All hot springs examined are used mainly for health purposes in Iran. Acanthamoeba were identified by both morphology and PCR (polymerase chain reaction). Genotype identification was based on the sequencing of a highly variable and informative region of Diagnostic Fragment 3 (stem 29–1 of 18S rRNA gene) within Acanthamoeba-specific amplimer (ASA.S1). Twenty percent of hot springs were contaminated with thermotolerant Acanthamoeba belonging to the potentially pathogenic T4 and T3 genotypes. A high number (91.7%) of strains showed growth at 37 °C, and eight isolates showed growth at 42 °C. A single isolate (HSNW2) was detected in waters at 70 °C. The presence of thermotolerant Acanthamoeba highlights a risk factor for susceptible individuals, as Acanthamoeba-related keratitis continues to rise in Iran. Periodic surveillance of thermal waters as well as improved filtration and disinfection is recommended to prevent disease related to pathogenic Acanthamoeba. This is the first comprehensive molecular study of Acanthamoeba genotypes in hot springs in Iran and the first to report the occurrence of the T3 genotype (corresponding to Acanthamoeba griffini) in thermal water sources in this country.

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