Rhododendron is the largest woody plant genus in the family Ericaceae, and northwestern Yunnan has been recognized as one of the diversification and differentiation centers of modern Rhododendron. However, the species classification is still a controversial issue due to their great morphological variations. The micromorphological characteristics of leaf abaxial surface have been recognized as the key identification features in Rhododendron. In the present study, the characteristics of scales and indumentums of 10 Rhododendron species from 6 subgroups in the subgenus Hymenanthes and Rhododendron collected from Yunnan Province were observed under scanning electron microscope (SEM). Furthermore, the clustering analysis was also conducted combined the results of the present study and the previous research in 45 species of Rhododendron plants to discuss the systematic significance of scales and indumentums in Rhododendron. Results showed that: (1) 8 species from subgenus Hymenanthes only have persistent indumentums in leaf abaxial surface, while 2 species from subgenus Rhododendron have densely scales. (2) The clustering analysis of 55 Rhododendron species based on the characteristics of leaf abaxial surface scales and indumentums indicated that the studied plants were divided into two clades distinctly. It is consistent with the traditional classification. Thus, we concluded that the characters of scales and indumentums of Rhododendron have an important taxonomic value at subgenus level. (3) At Subsection level, the characteristics of leaf abaxial surface scale and indumentums could be used among Subsect. Fortunea, Subsect. Maddenia and Subsect. Irrorata for classification. However, these features could not be used as key traits for classification of Subsect. Triflora, Subsect. Lapponica, Subsect. Taliensia, Subsect. Grandia and Subsect. Arborea in Rhododendron. (4) The clustering analysis also indicated that R. scabrifolium has close relationship with other species which have scales in leaf abaxial surface. Therefore, R. scabrifolium could be classified into the Subgen. Rhododendron.