The Owl clan is a squad of men within Shishio Makoto's rebel army who have been selected for their naturally high night-vision and trained to act as a team of night-raiding onmitsu. In the summer of 1878, under the orders of Sadojima Hōji, the Owl clan infiltrated the Kyoto headquarters of the Oniwabanshū in order to interrogate their leader Kashiwazaki Nenji regarding the whereabouts of the elusive Himura Kenshin. However, the Owl clan found themselves outmatched by their opponents and were all but wiped out. The squad leader returned to Mt. Hiei the morning after the attack, having been tortured through the night and with a message to Juppongatana associate Shinomori Aoshi carved into his back.

The Owl clan members dress in loose-fitting black onmitsu fuku with hoods and veil-like masks over their faces. Their left forearms are covered in an armor-like binding which end in sharp claws. Where the normal members are marked with grey bands, the squad leader is marked with red.