We present a complete sequence and describe the mitochondrial genome organization of the strain of small vannellid amoeba isolated from the Niagara River (Canada) in the year 2007. The circular mitochondrial DNA of this strain has 52, 924 bp in length and contains 30 protein-coding genes, two ribosomal RNAs, 25 transfer RNAs, and 13 open reading frames. It is the second in length mt genome among amoebae of the order Vannellida (Amoebozoa, Discosea). In contrast with the shorter mitochondrial genomes of crown vannellids, it shows no evidence of RNA editing. This finding supports the hypothesis on the independent origin of editing in the phylogenetic lineage corresponding to the order Vannellida (Amoebozoa, Discosea).