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In this study, we assembled the complete mitochondrial genome of Balitora ludongensis, based on high-throughput Illumina sequencing. The complete mitochondrial genome of B. ludongensis was 16,576 bp in size. It was made up of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region. Molecular phylogenetic analyses using 13 protein-coding genes revealed the phylogenetic position of B. ludongensis in Balitoridae. These data provide basic genetic information for B. ludongensis, which is vital for a better understanding of the mitogenomic diversities and evolution of fish species in Balitoridae.