We describe the complete sequence and organization of the mitochondrial genome from a brackish-water amoeba Clydonella sawyeri (Amoebozoa, Discosea, Vannellida). The circular mitochondrial DNA of this species has 31,131 bp in length and contains 17 protein-coding genes, 2 ribosomal RNAs, 21 transfer RNAs and 13 open reading frames. Length and gene content distinguish mitochondrial genome of Clydonella sawyeri from the mitochondrial genomes of other Amoebozoa species.