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Here, we assembled 58 mitogenomes representing 19 families and combined them with 10 published genomes to analyse 68 water mite taxa, the most extensive mitogenomic sampling assembled for the group to date. To test the robustness of higher\u2010level relationships, we compared three sequence matrices under three substitution\u2010model strategies and evaluated backbone congruence against a supermatrix incorporating legacy 18S, 28S and COI data. Across the nine mitogenomic analyses, Hydrachnidia was consistently recovered as monophyletic, with Eylaoidea sister to all remaining water mites. Hydrachnoidea was recovered as the earliest diverging lineage within Neohydrachnidia, whereas relationships among several deeper lineages, including the Hydryphantoidea grade, Lebertioidea, Arrenuroidea and Hygrobatoidea, remained sensitive to analytical treatment. Sixteen mitochondrial gene\u2010order configurations were identified, with rearrangements concentrated near the control region and involving tRNA loci more frequently than protein\u2010coding genes. Ancestral\u2010state reconstructions of mitochondrial gene order and five morphological character systems (coxal\u2010plate fusion, acetabular number, C4 glandularia position, swimming seta position and cuticle texture) showed that the phylogenetic informativeness of traditional classification characters differed among traits, with repeated state transitions inferred for some characters across water mite lineages. These results distinguish recurrent phylogenetic signals from model\u2010sensitive relationships and provide an expanded comparative framework for evaluating mitochondrial genome evolution and character change in Hydrachnidia.<\/jats:p>","DOI":"10.1111\/cla.70061","type":"journal-article","created":{"date-parts":[[2026,8,22]],"date-time":"2026-08-22T05:59:45Z","timestamp":1787378385000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["From genomic conflict to ecological adaptation: reconstructing higher\u2010level phylogenetic relationships of water mites (Hydrachnidia) based on mitochondrial genomes"],"prefix":"10.1111","author":[{"given":"Ping","family":"Li","sequence":"first","affiliation":[{"name":"Institute of Entomology, Guizhou University, Scientific Observing and Experimental Station of Crop Pests in Guiyang, Ministry of Agricultural and Rural Affairs of the P. R. China  Guiyang P. R. 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