Arachnids are an important group of arthropods. They are: diverse and abundant; a major constituent of many terrestrial ecosystems; and possess a deep and extensive fossil record. In recent years a number of exceptionally preserved arachnid fossils have been investigated using tomography and associated techniques, providing valuable insights into their morphology. Here we use X-ray microtomography to reconstruct members of two extinct arachnid orders. In the Haptopoda, we demonstrate the presence of ‘clasp-knife’ chelicerae, and our novel redescription of a member of the Phalangiotarbida highlights leg details, but fails to resolve chelicerae in the group due to their small size. As a result of these reconstructions, tomographic studies of three-dimensionally preserved fossils now exist for three of the four extinct orders, and for fossil representatives of several extant ones. Such studies constitute a valuable source of high fidelity data for constructing phylogenies. To illustrate this, here we present a cladistic analysis of the chelicerates to accompany these reconstructions. This is based on a previously published matrix, expanded to include fossil taxa and relevant characters, and allows us to: cladistically place the extinct arachnid orders; explicitly test some earlier hypotheses from the literature; and demonstrate that the addition of fossils to phylogenetic analyses can have broad implications. Phylogenies based on chelicerate morphology—in contrast to molecular studies—have achieved elements of consensus in recent years. Our work suggests that these results are not robust to the addition of novel characters or fossil taxa. Hypotheses surrounding chelicerate phylogeny remain in a state of flux.