Abstract:[Background] Qinghai harbors rich wild Morchella resources, whereas studies remain to be carried out for the species identification and characterization. [Objective] To identify a wild Morchella strain collected from Qilian, Qinghai and analyze its biogeography. [Methods] The morphological characteristics were combined with genealogical concordance phylogenetic species recognition and the phylogenetic analyses to identify the Morchella strain. Furthermore, species divergence time was analyzed and the geographic ancestral region was rebuilt. [Results] The strain MQL-1 presented a yellow-brown domed cap and a white hollow stalk, with a spore size of (21.17±4.33) μm×(14.26±3.25) μm and a hyphal diameter of (13.95±3.19) μm. Strain MQL-1 had 99% ITS sequence identity with Esculenta clade of the genus Morchella, and the genealogical concordance phylogenetic species recognition identified MQL-1 as Morchella crassipes. The estimated divergence time and reconstructed geographic ancestral region indicated that M. crassipes MQL-1 diverged from M. crassipes M10 at approximately 12.75 Mya (million years ago), and its most likely reconstructed geographic ancestral region was India (52.49%). [Conclusion] We isolated and identified a wild Morchella strain in Qinghai. This study enriched the information database of Morchella resources in Qinghai, laid a foundation for the follow-up work, and provided new ideas for fungal research.