The complete mitochondrial genome of Eleutheronema tetradactylum was determined, which was the first complete mitochondrial genome in Polynemidae family. The mitochondrial genome was 16,474 base pairs in length, encoding a standard set of 13 protein-coding genes, 2 ribosomal RNA genes, 22 tRNA genes and 2 main non-coding regions (the control region and the origin of the light strand replication). The overall base composition of E. tetradactylum is A 27.2%, C 29.9%, G 17.0% and T 25.9%, with a slight A + T bias of 53.1%. The mitochondrial genome of E. tetradactylum had common features about gene arrangement and tRNA structures compared with those of other vertebrate fishes. Two non-coding regions were also determined within its mitogenome. These mitogenome sequence data would play an important role in population genetics and phylogenetic analysis of the Polynemidae.