One of the most phylogenetically enigmatic taxa of Trombidiformes is the supercohort Eupodides (=Eupodina) consists of five superfamilies: Bdelloidea, Eriophyoidea, Eupodoidea, Halacaroidea, and Tydeoidea. However, this taxonomic system has not been supported by formal reconstruction of the phylogeny of these mite groups. In this paper, we present the results of the phylogenetic relationships of major lineages of Eupodides based on 18S rDNA, 28S rDNA, and COI sequences. By critically analysing the key morphological features of the mite taxa indicated by molecular analysis as the main eupodine lineages, we reconstructed a cladogram showing the cladistic hypothesis of the internal phylogenetic structure of Eupodides. Subsequently, the result was compared to the character evolution course suggested by tracing the morphological characters of eupodine mites on the reconstructed molecular tree. According to our data, Eupodides should still be classified as a monophyletic taxon grouping representatives of Bdelloidea, Eupodoidea, Tydeoidea, and Eriophyoidea; however, the taxonomic status of some superfamilies was not confirmed. Particularly, only the bdelloid clade with Cunaxidae nested within Bdellidae may correspond to the superfamily in the current taxonomic view. Additionally, the superfamilies Eupodoidea and Tydeoidea were demonstrated to be paraphyletic. Moreover, morphological, as well as molecular, data recovered Eriophyoidea nested within Tydeoidea.