Acariformes (one of the two main lineages of Acari) represent an exceptionally diverse group of Arachnida. We performed first comprehensive phylogenetic analysis of Acariformes using sequence data from the nuclear small subunit rRNA gene (18S rDNA) and the mitochondrial cytochrome c oxidase subunit I (COI, amino acids). Our analyses confirm the monophyly of Acariformes and recognize two orders within Acariformes: Sarcoptiformes, consisting of Endeostigmata and Oribatida+Astigmata, and Trombidiformes. The data revealed the origin of Astigmata within Oribatida with the desmonomatan superfamily Crotonioidea as the source of astigmatan radiation and the sexual family Hermanniidae as the sister group, which generally supports previous morphological hypotheses. These results were found despite the strong conflict between long-branch attraction (LBA) artifacts and phylogenetic signal. It is likely that the conflict resulted from differences in the substitution rates among acariform lineages, especially comparing slowly evolving Oribatida with rapidly evolving Astigmata. The use of likelihood methods considered more resistant to LBA only slightly decreased the chance of falling into the LBA trap; the probability of recovering the origin of Astigmata within Desmonomata differs only by about 10% from that of having the long branched Astigmata and Trombidiformes either connected directly or shifted to deep parts of the tree due to outgroup attraction. Molecular dating using the rate-smoothing method PATHd8 shows that Acariformes originated c. 435 MYA and were probably among the earliest arthropods invading terrestrial habitats in late Silurian or the Lower Devonian, when the first vascular plants are thought to have arisen. Our analyses did not support the monophyly of Acari because we recovered clades Acariformes-Solifugae and Parasitiformes-Pseudoscorpionida. However, a formal revision of arachnid classification that would reflect these results must await future analyses.