Abstract: In order to identify the pathogens of sugarcane rust disease, which observed on sugarcane new cultivars in Yunnan demonstration site of the national sugarcane system in 2014. By using field symptom observation, urediniospore morphology and molecular identification method to determine the sugarcane rust pathogens of 20 rust samples. Identification results showed that 4 rust samples of new sugarcane variety Haiyin1 collected from Menghai, Yunnan were confirmed to be sugarcane orange rust disease, the pathogen were identified to be Puccinia kuehnii Butler., their sequence shared more than 99.9% sequence identity with other reported isolates of P. kuehnii (GenBank Accession No.GU058021 and GQ283004-GQ283009), and were clustered into one group in phylogenetic tree. Sixteen rust samples of new sugarcane varieties/clones collected from Baoshan, Lincang and Menghai in Yunnan were confirmed to be sugarcane brown rust disease, their pathogens were identified to be Puccinia melanocephala Syd. et P. Syd., they had sequence similarities of over 99.8% with other reported isolates of P. melanocephala (GenBank Accession No.EU164548, GU058001 and JX036025), and in the same branch in phylogenetic tree. This is the first report of sugarcane orange rust disease caused by P.kuehnii in Yunnan sugarcane field.