A Naegleria strain harbouring two different populations of bacterial endocytobionts, together inhibiting the encystation of their host was isolated from a garden pond. Interestingly, the ability to form cysts was regained after removing one endocytobiont by antibiotic treatment. The trophozoite and the flagellate stage were investigated by light and electron microscopy and the temperature tolerance, underagarose migration and tissue culture pathogenicity of the strain were assessed. Moreover, the entire gene of the SSU rRNA was sequenced and compared to published sequences of various Naegleria species and a cluster analysis was performed in order to reveal the phylogenetic position of this endocytobiont harbouring Naegleria strain. The amoeba was shown to grow well at 37℃, to migrate under-agarose and to lyse human HEp-2 cells, properties related to pathogenicity. With the help of SSU rDNA sequencing and subsequent cluster analysis the strain N_DMLG was identified as N. clarki. The N. clarki strains altogether formed a cluster with N. gruberi and the potentially pathogenic N. italica, N. australiensis and N. tihangensis.