Background: Myiasis is a common disease occurring in humans and livestock all over the world. It is closely related to human society and of great significance to animal husbandry, forensic science, and medicine. Myiasis is known to occur in wild animals, while no information is reported in forest musk deer. On July 6, 2019, we found severe traumatic myiasis of an injured forest musk deer (Moschus berezovskii) (Flerov, 1929), infected by lots of maggots and clusters of eggs. However, the precise identification of the larvae that we collected was difficult with few specific morphology characteristics.Methods: DNA barcoding is an efficient technique for species diagnosis, therefore is employed to identify the samples collected from the infected forest musk deer. Firstly, we extracted genomic DNA from one larva and one egg respectively. The cytochrome oxidase I (COI) gene barcoding region was amplified by polymerase chain reaction (PCR) and bidirectionally sequenced by Sanger sequencing. The sequences were searched for similarity using BLAST and the best hits were Lucilia. To identify these blowflies accurately, these newly generated sequences were subsequently analyzed with COI sequences of Lucilia and Calliphora downloaded from GenBank, to calculate nucleotide divergence, and to construct a neighbor-joining tree.Results: Our results suggest that nucleotide divergence between the two samples is 0.0033cM, between two samples and Lucilia caesar (Diptera: Calliphoridae) (Linnaeus, 1758) is 0.0016–0.0050cM. Furthermore, the NJ tree construction indicates that the flies collected from the musk deer are Lucilia caesar.Conclusions: Our results indicate that DNA barcoding can successfully identify pathogenic species. As far as the authors know, this is the first time that myiasis is detected in forest musk deer caused by a traumatic infection in China. The affected individual was clinically treated immediately and apparently recovered.