The phylogenetic relationships among Citrus reticulate 'Gonggan' and partial Citrus were investigated by random amplified polymorphism DNA (RAPD). 10 primers generated 87 bands, with an average of 97.7% polymorphic bands. Dendrogram was drawn by the genetic similarity among the materials tested, which could help to clearly distinguish the relationships among different species, breeds and lines. The genetic background of Citrus reticulate 'Gonggan' was analyzed primarily as well, the results supported the view that Citrus reticulate ' Gonggan' was a natural hybrid of orange and tangerine more emphasis on tangerine which originating from Sihui region.