Among the living chordates there is little doubt that lancelets are most closely related to the Craniates based on synapomorphies such as segmented axial muscles and metameric organization of the visceral (pharyngeal) arches. Uniquely, the notochord of cephalochordates extends to the tip of the snout, the gonads are segmentally organized, adults have a high number (50+) gill arches, and there is a hood-like atrium covering the pharyngeal region. The Early Cambrian fossil Yunnanozoon possesses the extended notochord and segmental gonads, but lack the atrium and increased number of gill arches."

[Chordata. John G. Lundberg. The Tree of Life Web Project. http://tolweb.org/tree?group=Chordata&contgroup=Deuterostomia. 1995.]

All lancelets are in a single family, Branchiostomidae.