The origins of the two main mite lineages, Acariformes and Parasitiformes, are contentious, being inextricably linked to the wider controversy surrounding early chelicerate evolution. The traditional chelicerate framework has been upended by phylogenomic analyses, with important implications for the early evolution of mites and other chelicerates. In the most taxonomically comprehensive phylogenomic datasets, Acariformes and Parasitiformes emerge as early-branching lineages that break off separately from the backbone topology, sometimes uniting with non-mite taxa. One of the most unexpected results of phylogenomic analyses (although this result was also obtained with Sanger data but widely dismissed) is the placement of horseshoe crabs within Arachnida in a more nested position than both mite lineages despite their earlier appearance in the fossil record. This is broadly congruent with morphology, as horseshoe crabs exhibit a more modified head formation than mites. The absence of mites and other early branching arachnids from the pre-Devonian fossil record can potentially be explained by minute body size, weak integumental sclerotization, and low population densities within the taphonomically unfavorable voids within mineral regolith. The relocation of horseshoe crabs and affiliated taxa (sea scorpions, synziphosurines, etc.) to a more nested position indicates that the origins of mites should now be reconsidered within the broader context of chelicerate origins. However, the traditional representation of early chelicerate evolution still persists, heavily relying on fossils under the tacit and likely erroneous assumption that the fossil record faithfully tracks early chelicerate history. Within this general framework, competing interpretations have proliferated, driven partly by differences in preferred character systems among research groups. Newly proposed transitional fossils (Mollisonia, Megachelicerax, etc.) often carry broad phylogenetic implications, causing recurrent and dramatic shifts in the positions of putative stem-group chelicerates. But if the earliest chelicerates were minute-bodied and lived in habitats unfavorable for fossilization, this entire fossil-centric framework collapses, and an interdisciplinary approach is needed that de-emphasizes transitional morphology and incorporates extant ecology and molecular phylogenomics. Mites may therefore have a pivotal role in reconstructing chelicerate origins. Their early-branching placements in phylogenomic analyses make them central to developing a more robust and conceptually coherent framework for understanding the deep history of Chelicerata.