As the endemic species of China, Aculamprotula scripta is one of the most imperilled freshwater mussels. In this study, the complete maternal mitochondrial genome of A. scripta was firstly determined. The genome (15688 bp) had a typical structure of invertebrate mtDNA. It contained 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 novel gender-specific ORF. The nucleotide composition of the genome had a base preference, with the overall A + T content of 62.91%. The phylogenetic analysis revealed that A. scripta belonged to Unioninae, and was closely related to A. tientsinensis and A. coreana.