Objective: To verify phylogeography and genetic structure of Acanthamoeba populations among the Iranian clinical isolates and natural/artificial environments distributed in various regions of the country.Methods: We searched electronic databases including Medline, Pub Med, Science Direct, Scopus and Google Scholar from 2005 to 2016. To explore the genetic variability of Acanthamoeba sp, 205 sequences were retrieved from keratitis patients, immunosuppressed cases and environmental sources as of various geographies of Iran.Results: T4 genotype was the predominant strain in Iran, and the rare genotypes belonged to T2, T3, T5(Acanthamoeba lenticulata), T6, T9, T11, T13 and T15(Acanthamoeba jacobsi).A total of 47 unique haplotypes of T4 were identified. A parsimonious network of the sequence haplotypes demonstrated star-like feature containing haplogroups IR6(34.1%) and IR7(31.2%) as the most common haplotypes. In accordance with the analysis of molecular variance, the high value of haplotype diversity(0.612–0.848) of Acanthamoeba T4 represented genetic variability within populations. Neutrality indices of the 18 S ribosomal RNA demonstrated negative values in all populations which represented a considerable divergence from neutrality. The majority of genetic diversity belonged to the infected contact lens and dust samples in immunodeficiency and ophthalmology wards, which indicated potential routes for exposure to a pathogenic Acanthamoeba sp. in at-risk individuals. A pairwise fixation index(FST) was from low to high values(0.024 33–0.418 92). The statistically FST points out that T4 is genetically differentiated between north-west, north-south and centralsouth metapopulations, but not differentiated between west-central, west-south, centralsouth, and north-central isolates.Conclusions: An occurrence of IR6 and IR7 displays that possibly a gene flow of Acanthamoeba T4 occurred after the founder effect or bottleneck experience through ecological changes or host mobility. This is the first systematic review and meta-analysis providing new approaches into gene migration and transmission patterns of Acanthamoeba sp, and targeting at the high-risk individuals/sources among the various regions of Iran. Objective: To verify phylogeography and genetic structure of Acanthamoeba populations among the Iranian clinical isolates and natural / artificial environments distributed in various regions of the country. Methods: We searched electronic databases including Medline, Pub Med, Science Direct, Scopus and Google Scholar from 2005 To explore the genetic variability of Acanthamoeba sp, 205 sequences were retrieved from keratitis patients, immunosuppressed cases and environmental sources as various geographies of Iran. Results: T4 genotype was the predominant strain in Iran, and the rare genotypes belonged to T2 A total of 47 unique haplotypes of T4 were identified. A parsimonious network of the sequence haplotypes demonstrated star-like feature containing haplogroups IR6 (Acanthamoeba lenticulata), T6, T9, T11, T13 and T15 (Acanthamoeba jacobsi) 34.1%) and IR7 (31.2%) as the most common haplotypes. In accordance with the analysis of molecular variance, the high value of haplotype pe diversity (0.612-0.848) of Acanthamoeba T4 represented genetic variability within populations. Neutrality indices of the 18 S ribosomal RNA published negative values ​​in all populations which represented a considerable divergence from neutrality. The majority of genetic diversity belonged to the infected contact lens and dust samples in immunodeficiency and ophthalmology wards, which showed potential routes for exposure to a pathogenic Acanthamoeba sp. in at-risk individuals. A pairwise fixation index (FST) was from low to high values ​​(0.024 33-0.418 92). The statistically FST points out that T4 is genetically differentiated between north-west, north-south and centralsouth metapopulations, but not differentiated between west-central, west-south, centralsouth, and north-central isolates. Conclusions: An occurrence of IR6 and IR7 displays that a gene flow of Acanthamoeba T4 occurred after the founder effect or bottleneck experience through ecological changes or host mobi lity. This is the first systematic review and meta-analysis providing new approaches into gene migration and transmission patterns of Acanthamoeba sp, and targeting at the high-risk individuals / sources among the various regions of Iran.