Melampus bidentatus is a complex of three cryptic species that are an important component of the salt marsh communities along the North American east coast and the Gulf of Mexico. We assembled the mitochondrial genome of Melampus bidentatus North from Illumina short read data using NovoPlasty and annotated it on the MITOS webserver. Additional sequences were downloaded from GenBank. The mitochondrial genome contains 36 genes, 24 on the forward strand and 12 on the reverse strand, with one tRNA gene that is usually present in Ellobioidea missing. Melampus bidentatus is one of three currently known Ellobioid species (one, Pedipes pedipes, related, the other, Myosotella myosotis, less so) who deviate from the otherwise uniform gene order within the Superfamily. These three species are also recovered outside the rest of the Ellobioidea in all mitogenome based phylogenies, which is not supported by other phylogenetic or morphological studies.