The complete mitochondrial genome of a stream-dwelling frog species Paramegophrys oshanensis was determined. This mitogenome was 17,747 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region (D-loop). The base composition of the light strand was 28.77% A, 29.85% T, 26.26% C, and 15.11% G. Compared with most other vertebrates, this mitogenome has some different features: a non-tandem duplication of tRNA-Met gene (forming tRNA-Met1 and tRNA-Met2 genes), the replacement of tRNA-Trp gene by a 72-bp noncoding region translocated from the cluster of WANCY to the back of Cytb gene, the translocation of tRNA-Val gene from the front of 16S rRNA to the back of tRNA-Met1 gene, and the translocation of tRNA-Pro gene from the front of D-loop region to the front of tRNA-Met2 gene. Three kinds of tandem repeats with size ranging from 71 to 92 bp were detected within D-loop region.