[Objectives]  The natural enemies of Gynaephora qinghaiensis should be fully exploited for biological control of G. qinghaiensis. [Methods]  A parasitic fly was collected from the pupal stage of G. qinghaiensis. The species was identified by morphological method combined with molecular markers of COⅠ gene, and its phylogenetic relationship was studied. [Results] The length of the amplified COⅠ gene was 571 bp, and the contents of A, T, C and G bases were 40.63%, 31.00%, 14.54% and 13.84%, respectively. The contents of AT and GC were 71.63% and 28.37%, respectively, showing obvious AT bias. The parasitic fly in G. qinghaiensis was unanimously identified as Chaetogena gynaephorae of the Tachinidae family based on morphology and molecular data. The species of Tachinidae, such as Exorista larvarum, Tachinomyia nigricans, Parasetigena silvestris, Phorocera obscura, Gueriniopsis setipes, Chetogena gelida, Chetogena tessellata, and Carcelia sp., were clustered and then grouped with Chaetogena gynaephorae, indicating that the Chaetogena gynaephorae collected in this study is not closely related to other Tachinidae species. In addition, the branch of Chaetogena gynaephorae was closer to the root of the phylogenetic tree than the other branches, indicating that this species diverged earlier. [Conclusion]  This study provides a standardized identification process for the molecular classification of parasitic flies in G. qinghaiensis and lays a foundation for their identification.