Gyrodactylus konovalovi is an ectoparasite on East Asia minnow Rhynchocypris lagowskii that is widely distributed in cold freshwater, the dispersal of this ectoparasite depends on host switching, and it is therefore a good model species to study parasite and fish phylogeographic patterns. We examined the phylogeography of G. konovalovi along with the distribution of its host in the Qinling Mountains in Central China. A total of 109 individuals collected from 21 localities were subsequently sequenced for 536 bp of a mitochondrial cytochrome oxidase subunit I (cox1) gene and 46 haplotypes were obtained. The ratio of substitution sites (dN/dS) was 0.015 and showed purifying selection. Haplotype diversity (h) was highest in the YP population, while nucleotide diversity ( π ) was highest in the TTG population. While h and π were lowest in the XYB population, except for ten populations. Phylogenetic trees based on BI, ML and MP methods and network analysis revealed that all haplotypes were consistently supported in four different lineages, indicating a significant geographic distribution pattern. There was a significant positive correlation between genetic differentiation (Fst) and geographic distance. The results of mismatch distribution, neutrality test and Bayesian skyline plot analyses showed that all lineages were stable without expansion during the Pleistocene, while the total population underwent population contraction during the late Pleistocene. The molecular clock calibration inferred that the most common ancestor was estimated to have emerged in the early to middle Pleistocene. Therefore, our study suggests that clearly phylogeographic distribution of G. konovalovi may be related to geological events such as orogenesis, drainage capture changes and vicariance, during the Pleistocene in the Qinling Mountains in Central China, while the population subdivision was hardly affected by climate fluctuation during the Pleistocene.