Conopiscius shares V-shaped myomeres with the co-occurring conodont Clydagnathus but instead of a complex oral apparatus it has only a single pair of conical elements, and structures resembling scales are associated with its myomeres. Moreover, the coarsely crystalline crown tissue typical for conodonts has not been identified in the Conopiscius elements, which show only a finely lamellar skeletal tissue. The gap between conodonts and Conopiscius may be filled by isolated elements of similar morphology and structure occurring in the Late Devonian. They reveal a very thin external layer developed mostly at the tooth tip and resembling conodont crown tissue. The pulp cavity is partially filled with layered or spherulitic phosphatic tissue of the kind known also in conodonts (basal filling tissue) and early vertebrates (lamellin). Conodont elements of similar morphology and representing uni-membrate oral apparatuses have not been previously reported from the Devonian or Carboniferous but occur near the Cambrian–Ordovician transition (Proconodontus) and in the Late Permian (Caenodontus). It is proposed that Conopiscius represents a mostly cryptic conodont lineage extending from the Early Ordovician to the Permian, instead of being directly related to the agnathans.