Pollen morphology has a certain conservation, so it is often used as a classification basis for plant resources. The observation of citrus pollen morphology can provide some references for citrus classification. The pollen of 28 citrus materials were observed by FEI Quanta 200 field emission scanning electron microscopy including Guoposhan wild Zhoupigan and Yuanju. The morphological characteristics of pollen equatorial view, polar view and exine ornamentation were analyzed by the SPSS and NTsys software. And then analyze their genetic relationship, and reveal their classification status and system evolution relationship. The results showed that the pollen of Zhoupigan and Yuanju is 4colpate type. (1) Both of their pollens are medium size and Zhoupigan is slightly bigger. The pollen of equatorial axis of Zhoupigan is (35.24±1.94)μm, the polar axis is (20.39±1.35)μm. The pollen of equatorial axis of Yuanju is (30.21±1.14)μm, the polar axis is (22.12±1.97)μm. (2) Their exine ornamentation is different, Zhoupigan has irregular circular or polygonal pollen mesh, but the pollen mesh of Yuanju is round or roughly round. The mesh size of Zhoupigan is (1.65±0.09) μm and the width of mesh ridge is (0.51±0.10)μm. The width of mesh ridge of wild citrus of Yuanju is (0.47±0.09)μm and the mesh size is (0.86±0.08)μm. (3) The results of cluster analysis showed that 28 tested materials were divided into 9 groups at genetic distance of 0.827, among which Guposhan wild Zhoupigan in group Ⅸ alone and clustered with group Ⅷ at genetic distance of 0.976 ［C. mangshanensis (pointed leaves) and C. mangshanensis (round leaves)］; Yuanju and 10 of them were clustered into group Ⅴ and Cenxisuanju at genetic distance of 0.07, and C. reshni at genetic distance of 0.10. It speculates that the pollen morphology of Zhoupigan is similar to that of the C. mangshanensis. While the pollen morphology of Yuanju is similar to that of C. reshni and Cenxisuanju. According to cluster analysis, it is speculated that there are certain phylogenetic relationships between the Zhoupigan and C. mangshanensis, and has primitiveness uniqueness. C. mangshanensis (Guoposhan wild Zhoupigan) is supposed to be an independent and true species within the genus citrus, or it is a separate genus other than Poncirus, Fortunella Swing and Citrus L.. The wild citrus of Yuanju and Cenxisuanju, C. reshni have a certain genetic relationship.From the original analysis of pollen morphology, it is inferred that Yuanju is more primitive than C. daoxianensis and C.tachibana.