Abstract: 【Purpose】In this research ,we analyzed the sequences of Morus ---ITS, TrnL-F and ps16, for the value of phylogeny. And with evaluation of 12 special mulberry resources, it can be the theoretical basis for development and utilization.【Method】A total of 67 mulberry genotypes were analyzed (DNA extraction, PCR amplification, sequencing, software splicing, alignment, removing non-sequence bases, analyzing Length and G + C% content, Informative sites), and B. papyrifera and C. tricuspidata worked as outgroup. A cladogram ,generated using MP, was built.【Result】Mulberry ITS (including 5.8S) the length of basic sequence is 576 bp, variation range of 576-590 bp, G + C% 59.55-62.25, 40 informative sites; Mulberry TrnL-F Intergenic sequence(including the tRNA-Leu intron)，the length of basic sequence is 923 bp, variation range of 920-924 bp, G + C% 33.69-34.13, 23 informative sites; rps16 intron ,the length of basic sequence is 929 bp, variation range of 923-929 bp, G + C% 32.51-32.72, 17 informative sites. The most possible evolutionary models were (GTR + G), (GTR) and (GTR + G) respectively. And the optimal evolutionary model of the 3-segment-combined analysis was (GTR + G). In the cladogram , Morus nigra is separated first, the rest is divided into two branches. BranchⅠis mulberry, including M.wittorum, M. mizuho M.mongolica, M.mongolica var.diabolica, M. Australis, M. Bombycis, M. Alba and M. atropurprea. BranchⅡ is arbor, including M. cathayana, M. Macroura, M. notabilis. Shennongjia of M.cathayana♀ (high-quality mulberry wood) falls under Branch Ⅱ, and other 11 Mulberry special resources fall under BranchⅠ.【Conclusion】TrnL-F and rps16 sequence information sites of Morus is limited, but combined with the ITS sequences, it can improve the branch map information sites, and make branch map more reliable. Based on ITS, TrnL-F; rps16 sequence MP, M. nigra (Xinjiang) is divided into a single branch, as the most primitive type. So we can evaluate special mulberry resources through cladogram building.

Key words: Morus, Special Mulberry, ITS, TrnL-F, rps16 sequence, Maximum Parsimony analysis, Affinity, Evaluation