The complete mitochondrial genome was sequenced from the Amur stickleback Pungitius kaibarae. The genome sequence was 16,505 bp in size, and the gene order and contents were identical with the same genera Pungitius sinensis and other previously reported fish mitochondrial genomes. Of 13 protein-coding genes (PCGs), 3 genes (CO2, ND4, and Cytb) had incomplete stop codons. The base composition of P. kaibarae showed anti-G bias (8.86%) on the third position of PCGs.