Water scavenger beetles (Coleoptera: Hydrophiloidea) exhibit remarkable adaptations to both aquatic and terrestrial habitats and play irreplaceable ecological roles, yet their higher-level phylogeny and the molecular basis of their adaptive evolution remain unresolved. Here, we sequenced four complete mitogenomes of C. unipunctatus from the Qinghai–Tibetan Plateau (QTP) and conducted a comprehensive mitogenomic analysis by integrating these new data with 22 publicly available Hydrophiloidea mitogenomes, representing three families and six subfamilies. Our analyses revealed highly conserved mitogenomic architecture across Hydrophiloidea, with structural variation confined to non-coding regions and AT content correlating with both habitat type and phylogenetic lineage. Phylogenetic reconstructions robustly resolved the higher-level relationships: Helophoridae and Hydrochidae formed the sister group to Hydrophilidae, within which Hydrophilinae and Sphaeridiinae were strongly supported as monophyletic clades. We detected positive selection in the energy metabolism genes cox3 and nad5 along the ancestral branch of the terrestrial subfamily Sphaeridiinae, providing the first molecular evidence linking mitochondrial adaptation to the aquatic-to-terrestrial habitat shift. However, no positive selection signals were found in high-altitude C. unipunctatus populations, suggesting that adaptation to extreme environments operates through alternative mechanisms (e.g., regulatory or structural variation) rather than protein-coding evolution. This study establishes a robust phylogenetic framework for Hydrophiloidea and reveals the diverse molecular pathways underlying their adaptive evolution, from protein-coding adaptation during aquatic–terrestrial shifts to non-coding responses in extreme high-altitude environments.
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