Evolution and relationship to other animals The evolutionary relationships of chaetognaths have long been enigmatic.
Charles Darwin remarked that arrow worms were "remarkable for the obscurity of their affinities". Chaetognaths in the past have been traditionally, but erroneously, classed as
deuterostomes by
embryologists due to deuterostome-like features in the embryo.
Lynn Margulis and K. V. Schwartz placed chaetognaths in the deuterostomes in their
Five Kingdom classification. However, several developmental features are at odds with deuterostomes and are either akin to
Spiralia or unique to Chaetognatha. The similarities between chaetognaths and nematodes mentioned above may support the protostome thesis—in fact, chaetognaths are sometimes regarded as a basal
ecdysozoan or
lophotrochozoan. 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 might have retained deuterostome characters inherited from early
bilaterian ancestors. Thus chaetognaths may be a useful model for the ancestral bilaterian. Studies of arrow worms' nervous systems suggests they should be placed within the protostomes. According to 2017 and 2019 papers, chaetognaths either belong to or are the sister group of
Gnathifera. and
Protosagitta spinosa Hu) and the Middle Cambrian
Burgess Shale of British Columbia (
Capinatator praetermissus.) A Cambrian
stem-group chaetognath,
Timorebestia, first described in 2024, was much larger than modern species, showing that chaetognaths occupied different roles in marine ecosystems compared to today. A more recent chaetognath,
Paucijaculum samamithion Schram, has been described from the
Mazon Creek biota from the
Pennsylvanian of Illinois. The enigmatic
Nectocaris, documented from the
Burgess Shale since 1910 and described in 1976, has been recognized as a stem-chateognath in 2025. Chaetognaths were thought possibly to be related to some of the animals grouped with the
conodonts. The conodonts themselves, however, have been shown to be dental elements of
vertebrates. It is now thought that
protoconodont elements (e.g.,
Protohertzina anabarica Missarzhevsky, 1973), are probably grasping spines of chaetognaths rather than teeth of conodonts. Previously chaetognaths in the Early Cambrian were only suspected from these protoconodont elements, but the more recent discoveries of body fossils have confirmed their presence then. There is evidence that chaetognaths were important components of the oceanic
food web already in the Early Cambrian.
Internal phylogeny Below is a consensus evolutionary tree of extant Chaetognatha, based on both morphological and molecular data, as of 2021. }} ==History==