Chaetognaths are transparent or translucent and are covered by a cuticle. They have fins and a pair of hooked, chitinous, grasping spines on each side of their heads that are used in hunting. The spines are covered with a hood when swimming. They have a distinct head, trunk and tail. All species are hermaphroditic, carrying both eggs and sperm. Some species are known to use the neurotoxin tetrodotoxin to subdue prey. They have some developmental similarities to nematodes. Although they have a mouth with one or two rows of tiny teeth, compound eyes, and a nervous system, they have no respiratory, circulatory, or excremental systems. Materials are moved about the body cavity by cilia. Waste materials are simply excreted through the skin and anus. Chaetognaths swim in short bursts using a dorso-ventral undulating body motion, where their tail fin assists with propulsion and the body fins for stabilization and steering. At least one species of chaetognath, Caecosagitta macrocephala, has bioluminescent organs on its lateral fins.
Chaetognaths are traditionally classed as deuterostomes by embryologists. Lynn Margulis and K. V. Schwartz place chaetognaths in the deuterostomes in their Five Kingdom classification. Molecular phylogenists, however, consider them to be protostomes. Thomas Cavalier-Smith places them in the protostomes in his Six Kingdom classification. The similarities between chaetognaths and nematodes mentioned above may support the protostome thesis - in fact, chaetognaths are sometimes regarded as a basal ecdysozoan. Chaetognatha appears close to the base of the protostome tree in most studies of their molecular phylogeny. This may explain their deuterostome embryonic characters. If chaetognaths branched off from the protostomes before they evolved their distinctive protostome embryonic characters, they may have retained deuterostome characters inherited from early bilaterian ancestors. Thus chaetognaths may be a useful model for the ancestral bilaterian.