There are about 69 species of Mangifera in the world, and 8 species are mainly distributed in China. The long history of mango cultivation in China has resulted in many natural hybrids with local characteristics. In the process of continuous coordinated development with the environment, the appearance of mango, such as branches, leaves and fruits, has changed to some extent, but its pollen has formed unique morphological characteristics while maintaining genetic conservatism and stability. In order to further study the taxonomic significance of the pollen morphology of mango plants and clarify the phylogenetic relationship between mango natural hybrids, this study carried out palynological research and genetic relationship analysis on mango germplasm based on the microscopic characteristics of pollen, and observed the pollen morphology and pollen exine ornamentation of 32 mango materials from two species of mango using scanning electron microscopy. On this basis, cluster analysis was carried out on six quantitative characters of pollen. The results showed that the pollen of 32 the mango germplasms belonged to N3P4C5 type. The polar view was 3-split triangle, and the red view was nearly elliptical. There were three germination grooves, which almost reached both ends; There were differences in the shape and size of pollen, the width of germination ridge, pollen ornamentation, the density and size of pollen outer wall mesh among the materials. Stripes or reticular ornamentation and pits were all over the surface of pollen grains. Most mango pollen belongs to reticular ornamentation. Mesh shapes were diverse, mainly circular and long, with rough ridges. Mesh distribution density varied among different materials. According to the cluster analysis of quantitative characters such as pollen grain size, pollen morphology, germination ridge width, mesh size and mesh density, the 32 mango germplasms could be divided into three groups when the similarity distance was 15. Mango resources from Southeast Asia, such as Machesu M. indica, Siam Mango M. indica, Ren He Carabao M. indica, were clustered into one group in the pedigree map, showing certain regional characteristics; Yun Nan Tu Mango M. indica, Bruce Mango M. indica and Amemwins No.26 M. indica with narrow germination ridge were divided into one type; M. persiciformis, collected M. persiciformis and common domestic M. indica. cultivation species were grouped into one group. The original wild species, Bai Hua M. indica, was grouped with No.1 M. persiciformis, No.2 M. persiciformis, No.3 M. persiciformis, and No.4 M. persiciformis. The resource had the characteristics of primitive and wild types. This study would provide palynological basis for the classification, genetic relationship and evolution of mango pollen morphology.