Gyrodactylus konovalovi is an ectoparasite on the Amur minnow (Rhynchocypris lagowskii) that is widely distributed in the cold fresh waters of East Asia. In the present study, the phylogeography of G. konovalovi and the distribution of its host in the Qinling Mountains are examined. A total of 102 parasite specimens was sequenced for the mitochondrial cytochrome oxidase subunit 1 (cox1) gene, and 43 haplotypes were obtained. The ratio of substitution sites (dN/dS) was 0.016 and indicated strongly purifying selection. Haplotype diversity (h) and nucleotide diversity (π) of suprapopulations of G. konovalovi varied widely between distinct localities from the Qinling Mountains. Phylogenetic trees based on Bayesian inference (BI), maximum likelihood (ML) and maximum parsimony (MP) methods and network analysis revealed that all haplotypes were consistently well-supported in three different lineages A, B, and C, indicating a significant geographic distribution pattern. There was a significant positive correlation between genetic differentiation (Fst) and geographic distance (P < 0.001). The results of mismatch distribution, neutrality test and Bayesian skyline plot analyses showed that lineages A and B underwent population expansion after the Last Glacier Maximum (LGM) during the Late Pleistocene, while the lineage C underwent population contraction during the Middle to Late Pleistocene. Based on the molecular clock calibration, the most common ancestor was estimated to have emerged in the Middle to Late Pleistocene. Our study suggests that a clearly phylogeography of G. konovalovi was shaped by climatic oscillation and geological events, such as orogenesis, drainage capture changes and vicariance, during the Pleistocene in the Qinling Mountains in central China.