Phylogenetic resolution of ancient rapid radiations has remained problematic despite major advances in statistical approaches and DNA sequencing technologies. Here we report on a combined phylogenetic approach utilizing transcriptome data in conjunction with Sanger sequence data to investigate a tandem of ancient divergences in the harvestmen superfamily Ischyropsalidoidea (Arachnida, Opiliones, Dyspnoi). We rely on Sanger sequences to resolve nodes within and between closely related genera, and use RNA-seq data from a subset of taxa to resolve a short and ancient internal branch. We use several analytical approaches to explore this succession of ancient diversification events, including concatenated and coalescent-based analyses and maximum likelihood gene trees for each locus. We evaluate the robustness of phylogenetic inferences using a randomized locus sub-sampling approach, and find congruence across these methods despite considerable incongruence across gene trees. Incongruent gene trees are not recovered in frequencies expected from a simple multispecies coalescent model, and we reject incomplete lineage sorting as the sole contributor to gene tree conflict. Using these approaches we attain robust support for higher-level phylogenetic relationships within Ischyropsalidoidea. ; all5_672loci_nexNexus alignments of 672 loci containing transcriptomic sequence data from Trogulus, Ortholasma, Hesperonemastoma, Acuclavella, and Sabacon.672lociCharacterizations_all5DyspnoiAn .xls file characterizing aspects of the 672 loci used in phylogenetic analyses, including: evolutionary rates and branch lengths, AT and AT3 content, bootstrap distributions, subsampled loci, hidden support analyses, and concordance factors.all5_672loci_concatRAxMLAlignment and partitions file for the concatenated RAxML analysis of 672 lociall5_672loci_PhyML-trees672 gene trees generated via PhyMLall5_672loci_PhyML-BootstrapTrees100 bootstrap trees for each of 672 loci analyses in Newick formatall5_672loci_MrBayes_treFilesA MrBayes consensus ...