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In order to resolve the long-standing controversy surrounding the relationships within the Triplophysa genus, we conducted an extensive analysis of the complete mitogenome of Triplophysa labiata using DNBSEQ short reads. Additionally, we reconstructed the phylogeny of the Nemacheilidae family using mitogenome data. By comparing all available mitogenomes within the Triplophysa genus, we gained valuable insights into its evolutionary history. Our findings revealed that the mitogenome sequence of T. labiata is circular, spanning a length of 16,573 bp. It encompasses 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region (D-loop). Among the PCGs, the start codon ATG was commonly observed, except in cox1, while the stop codons TAA/TAG/T were found in all PCGs. Furthermore, purifying selection was evident across all PCGs. Utilizing maximum likelihood (ML) methods, we employed the 13 PCGs and the concatenated nucleotide sequences of 30 Triplophysa mitogenomes to infer the phylogeny. Our results strongly supported the division of the Triplophysa genus into four primary clades. Notably, our study provides the first evidence of the close relationship between T. labiata and T. dorsalis. These findings serve as a significant foundation for future investigations into the mitogenomics and phylogeny of Nemacheilidae fishes, paving the way for further advancements in this field of research. [ABSTRACT FROM AUTHOR]