The ITS sequences of Morus were analyzed in this study, which have an average length of 576 bp and a GC content of 59.55%. There are many mutations in the ITS sequences, and a total of 166 variants are identified (100 in ITS1, 60 in ITS2, and 0 in 5.8S). The systematic location of Morus is between Milicia excelsa (MEU93585) and Streblus heterophyllus (DQ499105), and much closer to the former one based on the maximum parsimony (MP) analysis. Under Bayesian analysis, Xinjiang M. nigra and North America M. murrayana (FJ605515) were firstly separated in cladogram as the most primitive species with the time of origin at about 55 mya, while other species were divided into three branches: (1) Lichuan M. wittiorum and Xianfeng M. wittiorum with a time of origin at about 2 mya; (2) M. cathayana related species with a time of origin at about 15 mya; (3) species that morphology related to M. alba with a time of origin at about 28 mya. Morus was originated from the high latitude regions in Laurasia and then migrated from north to south. The mountains between 20-40°N latitudes in East Asia are the secondary origin centers of Morus.