Project description:In this study, we obtained the complete mitochondrial genome of Hypseleotris cyprinoides, which was 16520 bp in length. The mitogenome contained 37 genes, including the typical set of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and 2 Ribosomal RNA (rRNA) genes. A, C, G, and T distribution was 28.57%, 29.91%, 16.99%, and 24.53%, respectively. The length of the total protein-coding genes was 11441 bp, which accounts for 66.80% of the whole mitochondrial genome. The Maximum Likelihood (ML) phylogenetic analysis based on the concatenated nucleotide sequences of 13 PCGs showed that H.cyprinoides as a sister species to Hypseleotris klunzingeri was clustered in the family Hypseleotris. The discovery of the complete mitochondrial genome of H.cyprinoides would help to conduct in-depth research on Hypseleotris.