Parabotia bimaculata is a common small-bodied endemic riverine loach in China. There was still no relevant genetic information for P. bimaculata. Here, we reported that the complete mitochondrial genome of P. bimaculata was a circular molecule of 16,588 bp in length, with two rRNA genes, 13 protein-coding genes, 22 tRNA genes, and a control region (D-loop). The gene composition and the structural arrangement were identical to the other Parabotia species and most of other teleosts. The nucleotide acid composition of the entire mitogenome was 30.8% for A, 27.9% for C, 16.1% for G, and 25.3% for T, with an A + T content of 56.1%. Phylogenetic analyses placed P. bimaculata in a well-supported monophyletic cluster with the other three Parabotia species in Botiidae.