Significant progress has been made in the understanding of family-level relationships among most major lineages of Mesostigmata. An exception to this is Uropodina, a lineage with a problematic classification and incomplete species descriptions. While recent efforts have been made in cataloging names of varying taxonomic levels, a stable and concrete classification system is still lacking. This is mainly due to the absence of a robust phylogenetic analysis for the group. Our study aims to address this by inferring the phylogeny of Uropodina using molecular data derived from the mitochondrial genome. Our taxon sampling included representatives of most biogeographic realms and a wide variety of habitats, covering 28 of the 31 recognized uropodine families. We attempted to assemble mitochondrial genomes from 91 samples sequenced using a low coverage whole genome skimming approach. Resulting assemblies were annotated to identify and extract sequences of the 37 mitochondrial genes. For phylogenetic analysis, we only included data from the 13 protein coding genes of the mitochondria. Tree inference using maximum likelihood and Bayesian methods were conducted on datasets that included varying taxonomic and gene coverage. Of the 91 samples sequenced, we assembled complete mitogenomes for 48 species and recovered fragments for all except 2 of the remaining samples. Complete mitogenome sizes ranged from 14,291-15,804 base pairs with relatively low GC content across all samples. Genes generally followed the known order of uropodines. We identified three main rearrangements characterized by the position of tRNAs C and P, as well as a few highly divergent gene orders. Maximum Likelihood and Bayesian trees showed strong support for monophyly of Uropodina, including Microgyniidae but not Protodinychidae (the position of Diarthrophallidae could not be established due to insufficient sequencing results). Resulting tree topologies suggest up to seven major groupings potentially representing superfamilies. These include a well-supported monophyletic Uropodoidea (sensu stricto) and a previously unrecognized clade of predominantly tropical distribution. This tropical clade included a subset of the problematic family Urodinychidae which appears to be polyphyletic. Lastly, the recognition of “higher Uropodina” characterized by the presence of a sclerotized node in the chelicera received no consistent support. Insights from our mitochondrial phylogenomic study are inconsistent with the current classification of Uropodina. However, a more robust revision of higher-level classification of the group will require integration of nuclear genomic and morphological datasets.