Aim and Background:Naegleria genus, flagellated amoebae that occur in soil and water and found in every climate zone. This parasite causes inflammation of the central nervous system primary amoebic meningoencephalitis, which is famous in it.
Material and methods:In this study water100 samples collected from the Tonekabon River. Samples filtering and cultured in performed modified Nelson media. After examining the morphology and stain, molecular identification was done.
Results:13 samples as recognizing the morphology of Naegleria spp. amoebae were detected using specific primers for amplification of 186 bp 18SrRNA and the accuracy of the diagnosis was confirmed. after sequencing, genotyping obtained belong to a new species Naegleria clarki.
Conclusion:The result indicates the presence of Naegleria clarki in this rivers cities. Given that the amoeba can cause transmission of pathogenic microorganisms responsible for this area, therefore, must take the necessary measures to overcome the pollution in the rivers.

Keywords: Naegleria fowleri, Naegleria clarki, Tonekabon Rivers, PCR

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