Consensus about the phylogenetic relationships of chelicerates has remain elusive despite the growing availability of genomic data. While the monophyly of orders is universally supported, there is much less consensus about how these groups relate to each other. Analyses based on morphological characters are portrayed as supportive for the monophyly of terrestrial arachnids and for a basally branching position of scorpions within Arachnida. By contrast, both of these hypotheses are typically rejected in molecular based phylogenies, including genomic analyses. Even within a specific data class, there is no agreement on the placement of neglected orders such as palpigrades, solifugids, and pseudoscorpions. We therefore sequenced phylogenetically significant lineages of Chelicerata using a transcriptomic approach, and thereafter compiled and analyzed a comprehensive dataset of representative chelicerate lineages. In addition, we coded a new morphological character matrix for Chelicerata, with the goal of characterizing nodes with heightening conflict between different data classes. Simultaneous analysis of the two data partitions enabled circumscription of the most recalcitrant parts of the chelicerate tree of life. The resulting tree topology facilitated reconstruction of major events in the evolutionary history of chelicerates, with emphasis on the evolution of respiratory and visual systems.