During a Chiroptera resource survey conducted in 2023 on the Pamir Plateau of China's Xinjiang Uygur Autonomous Region, two adult male bat individuals were captured. External morphology examination revealed small-sized individuals characterized by long, narrow ears with straight tragus structures tapering to sharp tips—features diagnostic of the genus Myotis. Concurrently, we obtained free-flight echolocation calls from the bats: the signals showed an initial frequency of 65.12 ± 2.12 kHz, terminal frequency of 42.78 ± 1.27 kHz, peak energy frequency of 47.41 ± 1.46 kHz, pulse duration of 2.52 ± 0.26 ms, and inter-pulse interval of 94.01 ± 31.41 ms. Based on skull morphological traits and bioacoustic data, the specimens were preliminarily identified as Myotis aurascens. However, our phylogenetic analysis based on the mitochondrial cytochrome b (Cytb) gene revealed that sequences attributed to M. aurascens and M. davidii formed a single strongly supported clade, underscoring the unresolved taxonomic status of these species. Irrespective of the exact species assignment, this discovery constitutes the first documented occurrence of the M. davidii/aurascens complex on the Pamir Plateau, thereby extending the known distribution range in China. Notably, these specimens represent the highest-elevation record for this group to date (3200 m). Our study provides the first comprehensive description of cranial morphology and echolocation signatures for this taxon in a high-altitude habitat. These findings significantly enhance regional biodiversity inventories and offer critical baseline data for plateau ecosystem research.