Despite being found in almost every habitat, exhibiting diverse morphologies and life histories and being extremely important as decomposers, moss mites or Oribatida still hide a lot of secrets. Studying their relationships and thus inferring the evolution of certain traits is crucial to further understanding these arachnids. A group closely related to Oribatida is the Astigmata, a well-studied group containing some major parasites and pests. Nevertheless, how these two large groups are related to each other has remained controversial. An overview on previous phylogenetic studies addressing this question is presented as well as new results from multiple tree inferences based on phylogenomic data. Already published as well as newly sequenced genomes and transcriptomes were used for phylogenetic analyses, aiming for a representative and comprehensive selection of taxa from all oribatid infraorders (including most oribatid superfamilies) and astigmatid mites. The analyses were conducted using combinations of five aligning and five trimming methods and two tree-inference methods plus additional Bayesian analyses. Difficulties which occurred during this study like long branch attraction and varying tree topologies between different methods and data subsets will be shown as well as novel findings on the relationship of Oribatida and Astigmata. The present study is based on 133 full genome and transcriptome data from Astigmata and Oribatida and additionally includes several acariform taxa as outgroups, in total representing the so far largest and most balanced taxon sampling for Acariformes. Our results not only indicate the evolutionary origin of Astigmata within Oribatida but also at a - so far never proposed - position within Mixonomata. Moreover, the internal phylogenetic relationships of the six main cohorts of Oribatida were revised in detail, with only two cohorts, namely Palaeosomata and Brachypylina, found monophyletic. The remaining four cohorts turned out to be paraphyletic. Comparably, all astigmatid superfamilies which were represented by more than one genus, emerged as polyphyletic. In conclusion, our results shed light on the longstanding question of oribatid and astigmatid phylogenetic relationships, as demonstrated on a reliable genomic/transcriptomic basis.