Kashmir musk deer, Moschus cupreus (KMD) is one the most threatened species endemic to the Himalayan region of Kashmir, Pakistan and Afghanistan. Herein, we have sequenced, annotated and characterized the complete mitogenome of M. cupreus. The investigation and comparison of the mitogenome provide crucial information for phylogenetic analysis to understand the evolutionary relationships. The mitogenome of KMD was 16,354 bp long, comprising 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and non-coding control region. Its composition was highly A+T biased 68.42%, and exhibited a positive AT–skew (0.082) and negative GC–skew (− 0.307). The phylogenetic analysis suggested that KMD was a primitive and extant species in the genus Moschus, whereas Alpine musk deer (M. chrysogaster) and Himalayan musk deer (M. leucogaster) were the closest relatives. It indicated the placement of M. cupreus within the monotypic family Moschidae of musk deer. Hence, it provides a better understanding of lineage identification and musk deer evolution for further research.

克什米尔麝香，Moschus cupreus（KMD）是克什米尔，巴基斯坦和阿富汗的喜马拉雅地区特有的最受威胁物种。在这里，我们已经测序，注释和表征了M. cupreus的完整的有丝分裂基因组。有丝分裂基因组的研究和比较为系统发育分析了解进化关系提供了重要信息。KMD的有丝分裂基因组长16354 bp，包括13个蛋白质编码基因（PCG），22个转移RNA基因（tRNA），两个核糖体RNA基因（rRNA）和非编码控制区。它的成分具有较高的A + T偏倚68.42％，并显示出正的AT偏斜（0.082）和负的GC偏斜（-0.307）。系统发育分析表明，KMD是该属的原始和现存种。麝香（Moschus），而高山麝（M. chrysogaster）和喜马拉雅麝（M. leucogaster）是最亲近的亲戚。它表明了M. cupreus在麝香单型家族Moschidae中的位置。因此，它为沿袭鉴定和麝鹿进化提供了更好的理解，以供进一步研究。