The complete mitogenomes of Cheilopogon unicolor , C. arcticeps and C. atrisignis were determined by the next-generation sequencing (NGS) method. The assembled mitogenome of C. unicolor , C. arcticeps and C. atrisignis consist of 16 529 bp, 16 530 bp and 16 530 bp, respectively. Three mitogenomes contain the typical gene complement including 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNA genes and a non-coding D-loop. The length of D-loop is 870 bp ( C. unicolor and C. arcticeps ) and 869 bp ( C. atrisignis ), located between tRNA-Pro and tRNA-Phe. Phylogenetic analysis indicates that Cheilopogon is not monophyly. The mitogenomes of C. unicolor , C. atrisignis and C. arcticeps may provide useful information for phylogentic and population genetic analysis for flyingfishes.

Background: Hirundichthys oxycephalus is an important flyingfish resource in eastern Taiwan and northwestern Japan. A substantial catch decline in Taiwan has caused serious concerns on stock status of the fish, prompting the government to impose a set of regulations on flyingfish egg fishery since 2008. However, the regulations were set in a precautionary manner, without considering the fundamental understanding of the population genetic structure. This study aims to investigate the population genetic structure of H. oxycephalus in the region based on mtDNA cytochrome oxidase I (COI) gene and to thus provide scientific information for sustainable management of the resource.