A new hypothesis of the relationships between arachnomorph arthropods, and the origin of chelicerates, is presented based on a cladistic analysis of 34 taxa and 54 characters. The present study provides a detailed discussion of primary hypotheses of homology and includes a more complete range of terminal taxa than previous analyses. The analysis provides the first convincing synapomorphies for the Arachnomorpha, and suggests that the marrellomorphs are not arachnomorphs. The assignment of Cambrian ‘great appendage’ (or megacheiran) arthropods to the Arachnomorpha is confirmed, and potential synapomorphies uniting them with chelicerates are discussed and tested. Principal amongst these are the loss of the first cephalic appendages (the antennae), loss of the exopods of the second cephalic appendages and modification of the endopods of these appendages into spinose grasping organs. The Arachnomorpha consists of two major clades: (1) a ‘chelicerate-allied’ clade, including chelicerates, megacheirans, Emeraldella, Sidneyia, cheloniellids and aglaspidids, in which chelicerates and a paraphyletic group of megacherian arthropods form the sister group to the remaining taxa; and; (2) a ‘trilobite-allied’ clade, including trilobites, xandarellids, helmetiids, tegopeltids and naraoiids, the relationships of which are more fully resolved than in previous studies.