Although they are widespread and include more than 6,000 species, water mites are understudied and many groupings below the genus level are believed not to be monophyletic. North American Arrenurus are divided into four subgenera: A. (Arrenurus), A. (Truncaturus), A. (Megaluracarus), and A. (Micruracarus). These subgenera (and the species therein) have largely been described based on male morphology. However, these character states sometimes grade into each other, blurring the lines separating these lineages. Further, female Arrenurus have generally been overlooked in species descriptions because they are morphologically conserved. This research sought to tackle this complicated taxon by focusing on North American A. (Micruracarus) and constructing molecular phylogenies using the mitochondrial gene, cytochrome c oxidase I (COI), and ultraconserved elements (UCEs). Both concatenated and multilocus coalescent methods were able to recover a well-supported molecular phylogeny for A. (Micruracarus) and suggested the subgenus is made up of four species groups. This research demonstrated that a large number of loci can be obtained from individual water mites and well-supported relationships above the species-level can be reconstructed using UCEs.