AbstractMitochondrial genome sequence of Vannella croatica (Amoebozoa, Discosea, Vannellida) was obtained using pulse‐field gel electrophoretic isolation of the circular mitochondrial DNA, followed by the next‐generation sequencing. The mitochondrial DNA of this species has the length of 28,933 bp and contains 12 protein‐coding genes, two ribosomal RNAs, and 16 transfer RNAs. Vannella croatica mitochondrial genome is relatively short compared to other known amoebozoan mitochondrial genomes but is rather gene‐rich and contains significant number of open reading frames.