Matsubarichthys inusitatus is described from a single specimen, taken from One Tree Island, Queensland, Australia. It is readily distinguished from other scorpaenoids by its unique dorsal-fin formula (II, IV, 6) and vertebral formula (9 + 12 = 21), both with fewer elements than previously reported for a scorpaenoid; a low anal fin-ray count (II,4); a pelvic fin-ray count of I,1; and the gill opening restricted to a pore dorsal to the opercle. Although the holotype is small (8.5 mm SL) and study of its internal anatomy thus limited, Matsubarichthys inusitatus is a relatively primitive aploactinid that can not be readily assigned to either of the two currently recognized aploactinid subfamilies, but may be a sister-group of the Bathyaploactininae.