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The complete mitochondrial genome sequence of Paragyrodactylus variegatus was determined and analyzed in this study.The size of the entire mitochondrial genome of P.variegatus is 14517 bp,containing 12 protein-coding genes (PCGs),22 transfer RNA (tRNA) genes,2 ribosomal RNA (rRNA) genes and a major non-coding region (NCR).The overall A + T content of the mitochondrial genome is 76.3%,which is the highest in the reported mitochondrial genome of monogenean.All PCGs use initiation codon (ATG),except ND1 and COII,which begins with GTG and TTG,respectively.TAA termination codon was found from 11 PCGs except ND5 which used the codon TAG.All of the 22 tRNAs have the typical cloverleaf secondary structure,except tRNACys,tRNASer1 and tRNASer2 lacking of dihydrouridine (DHU) arm.There are six domains (domain Ⅲ is absent) and three domains in the inferred secondary structures of large ribosomal subunit (rrnL) and small ribosomal subunit (rrnS),respectively.The NCR includes 6.1 40 bp tandem repeat units and the double identical poly-T stretches,stem-loop structure and some surrounding structure elements.There is a different gene order (tRNAGln,tRNAMet and NCR) relative to the arrangement of mitochondrial genome of Gyrodactylus spp.The Duplication and Random Loss Model and Recombination Model together are the most plausible explanations for the evolution of that variation.All the morphological characters and characteristics of mitochondrial genome support Paragyrodactylus is a separate genus from Gyrodactylus.Considering their specific distribution and host,we tended towards the view that Paragyrodactylus is a relict freshwater lineage of viviparous monogenean isolated in the high plateaus of central Asia on at least three genera of closely related river loaches.