Gyrodactylus nigeri Zhou & Chen, 2024 was merely distributed in Yunnan Province, Southwest China; meanwhile, its mitochondrial genome remains unclear. This study aims to sequence the mitogenome of G. nigeri and clarify its phylogenetic relationship within the Gyrodactylidea. The mitogenome of G. nigeri was sequenced using the next-generation sequencing (NGS) method, annotated, and analyzed using bioinformatic tools. The mitochondrial genome of G. nigeri is 14,903 bp in length, containing 12 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and two major non-coding regions (NCR: NC1 and NC2). The overall A+T content of the mitogenome is 76.6%, a higher content compared with all reported mitochondrial genomes of monogeneans. The mitogenome of G. nigeri presents a clear bias in nucleotide composition with a negative AT-skew and a positive GC-skew. All tRNAs have the typical cloverleaf secondary structure except for tRNACys, tRNASer1, and tRNASer2, which lack the dihydrouridine (DHU) arm. Furthermore, two different repetitive non-coding regions of 88 bp repeats occurred in the NCR regions (NC1 and NC2) with a poly-T stretch, two stem-loop structures with obvious differences in the first loop, and a G(A)n motif. The gene order is identical to the mitochondrial genomes reported from other Gyrodactylus species except Gyrodactylus sp. FZ-2021.Co-phylogenetic analyses showed divergence patterns of Gyrodactylus correspond to those of their fish hosts, and the overall coevolutionary fit between the parasites and hosts was consistently significant. Meanwhile, the results supported the sister relationship between G. nigeri and Gyrodactylus sp. FY-2015 from the hosts within the Nemacheilidae cluster together with high nodal support based on 12 PCGs sequences and amino acid sequences. Gyrodactylidae forms an independent and monophyletic clade within Gyrodactylidea.