Phylogenetic relationships and evolutionary patterns within the arachnid order Solifugae are poorly understood and largely unresolved due to conserved morphology and scarce genomic resources. In this study, we evaluated the role of restriction endonuclease (RE) selection in double-digest restriction-site-associated DNA sequencing (ddRADseq) as a methodology for exploring the evolutionary history of solifuges and their responses to changing desert landscapes and climate. We optimized this method by using computer simulations to explore the effect of different enzyme combinations on the process in silico. Genome data are not yet available for Solifugae, so we performed the simulations using available spider, scorpion, tick, mite and xiphosuran genomes. Guided by the simulations, we then pioneered ddRADseq in Solifugae by generating data for four samples representing two families and three genera. Our results highlight the utility of simulated data and give us confidence that ddRADseq will be ideal for studying the evolution of solifuges.