The complete mitochondrial genome was sequenced from the freshwater gudgeon, Gobiobotia nakdongensis. The genome sequence was 16,609 bp in size, and the gene order and contents were identical with other previously reported fish mitochondrial genomes. Of the 13 protein-coding genes (PCGs), 3 genes (CO2, CO3, and Cytb) had incomplete stop codons. The base composition of G. nakdongensis showed anti-G bias (9.93%) on the third position of PCGs.