Idiosepius pygmaeus, also known as the Two-toned Pygmy Squid, is a species of bobtail squid native to the Indo-Pacific.
We report the first complete mitochondrial genome of the pygmy squid, Idiosepius, (Idiosepiidae). The mtDNA genome is 16,183 bp long with an AT content of 75.4%. All conserved metazoan mitochondrial genes are identified with the addition of a 1018 bp non-coding region. Idiosepius gene order most closely resembles that of the bobtail squid Semirossia (Sepiolidae)