The Cambrian fossil Amiskwia sagittiformis has puzzled palaeontologists for more than a century, but recent re-investigation of its morphology suggested a close relationship with the bilaterian clade Gnathifera, comprising Rotifera, Gnathostomulida and Micrognathozoa. Since Amiskwia has already been considered closely related to Chaetognatha, this new interpretation of its morphology supports recent molecular and developmental studies finding a close phylogenetic relationship between Chaetognatha and Gnathifera. The recent re-description of the jaw apparatus of Amiskwia with the first phylogenetic analysis by Vinther & Parry (2019) found a rather surprising topology with Amiskwia and Chaetognatha being sister groups and nested inside Gnathifera. Furthermore, a subsequent paper from Caron & Cheung (2019) re-described the jaws of Amiskwia as very similar to the configuration found in Gnathostomulida, but did not include any phylogenetic analysis. Here we test the topology of Vinther & Parry with various parsimony and Bayesian analyses, taking into account the new description of Caron & Cheung with careful re-amendment of the matrix of Vinther & Parry. According to our results and the recent findings on the molecular phylogeny of their extant members, we suggest a new systematization of these taxa. We recovered Amiskwia as a stem-group chaetognath within a clade Cucullophora nov., rejecting the Caron & Cheung hypothesis of its close affinity to Gnathostomulida, and found a more consensual topology with monophyletic Gnathifera sister group to Cucullophora, all together forming the clade Chaetognathifera. Furthermore, Rotifera + Micrognathozoa form a clade named Gynognathifera nov. We discuss the characters supporting each clade and the reasons that account for the topology found by Vinther & Parry. Finally, we hope that this carefully amended matrix focused on Gnathifera, Amiskwia and Chaetognatha, together with a formal classification and robust phylogeny, will be of use for future studies on the palaeontology and morphology of these clades.