To better understand the genetic diversity and phylogeny of Coilia, the complete mitochondrial genomes of two lineages in Coilia mystus were compared. They were all typical circular double stranded DNA molecule with 17075 bp in C. mystus N and 16964 bp in C. mystus S, respectively, containing the standard metazoan set of 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and non-coding regions. The mitogenomes of C. mystus N and C. mystus S shared the identical structural organization and gene arrangement with those of other Coilia fishes. Both lineages of C. mystus showeda similar features in not only the strand-specific asymmetry of nucleotide composition, but also the codon usage of genes. Whereas a significant variation among Coilia species was detected in length of the control region, mainly caused by the variable number of tandem repeats. Phylogenetic analysis was performed based on 13 concatenated mitochondrial protein-coding genes from 8 Coilia mitochondrial genomes. The results supported that C. lindmani at first clustered with C. nasus and C. grayii which had close relationships (d=0.028), then clustered with C. mystus which exhibited obvious genetic differentiation between C. mystus N and C. mystus S (d=0.083). C. reynaldi was at the basal part of the trees, and showed obvious genetic differentiations with other Coilia species (d>0.19). Our results suggested that the north and south lineages of C. mystus could be genetically distinct as different species.