Comparative Analysis of Mitogenomes of <em>Microtendipes</em> (Diptera: Chironomidae) and Its Phylogenetic Implications

Insect mitochondrial genomes are pivotal for understanding evolutionary relationships and species identification. This study focuses on Microtendipes (Chironomidae), a genus with unresolved phylogenetic positioning and cryptic species challenges. We sequenced and analyzed eight mitogenomes from five Microtendipes species, integrating 18 published Chironominae mitogenomes to reconstruct phylogenies using Maximum Likelihood and Bayesian Inference. The mitogenomes exhibited conserved gene arrangements but variable control region lengths (338–1,266 bp) and high AT content (94.14–96.42% in control regions). Comparative analyses revealed significant intraspecific genetic distances (5.3–13.8% across 13 protein-coding genes), challenging COI-based barcoding for species delimitation. Phylogenetic reconstructions resolved Microtendipes as a distinct clade, refuting its inclusion in the Polypedilum complex. Notably, larval morphology-based species groupings conflicted with molecular data, suggesting cryptic diversity. Our results support Microtendipes as a potential independent tribe within Chironominae, highlighting mitogenomes’ utility in resolving taxonomic uncertainties. This study advances the evolutionary understanding of Chironomidae and underscores the limitations of single-gene barcodes in species-rich genera.