The paddy frog (Fejervarya multistriata) belonging to the family Dicroglossidae, is a species widely distributed in temperate and tropical Asia. In this study, the complete mitochondrial genome of F. multistriata was sequenced. The mitogenome was 17 677 bp in size, consisting of 13 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a non-coding control region (D-loop). Like in other vertebrates, most mitochondrial genes of the species are encoded on the heavy (H) strand, except for ND6 and eight tRNA genes which are encoded on the light (L) strand. The overall base composition contained 28.03% A, 29.90% T, 26.91% C and 15.16% G. The alignment of the Fejervarya and related species' control regions exhibited high genetic variability and rich A + T content. In addition, we found that the tRNA-Leu2 rearrangement occurred in the LTPF gene cluster in the mitochondrial genome of the F. multistriata, resulting in a new arrangement (T-PL-F). There was a tandem duplication of the tRNA-Met gene between tRNA-Gln and ND2, and the similarity rate of the two genes reached 74.6%. The phylogenetic relationships based on nucleotide sequences of 13 PCGs was analysed by re-establishing phylogenetic trees (ML and BI). The results indicated that F. multistriata was more closely related to F. limnocharis than to F. cancrivora and F. manoharani, the two latter showing a new gene rearrangement (ND6-tRNA-Glu-Cytb-D-loop-ND5-tRNA-Thr-tRNA-Pro-tRNA-Leu-tRNA-Phe). Our results indicate that F. limnocharis sample found in Yancheng, and F. multistriata from Mojia, Santai and Ji'an, are possible conspecifics. This study on the mitochondrial genome of F. multistriata provides an important reference for the future studies on phylogenetic relationship and the taxonomic status of Fejervarya and related Dicroglossidae species.