Abstract: The investigation on ultrastructural features and cytological features of infection process for southern corn rust fungus (Puccinia polysora Underw) would provide an important basis for understanding its pathogenesis and rust resistance mechanisms of maize. The natural infected corn leaves of southern rust fungus from two maize varieties ‘Zhengdan 958’ and ‘Xianyu 335’ were collected and the samples were vacuumed and immobilized using 4% glutaraldehyde. The processed samples were then investigated by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The results indicated that: the intercellular hyphae of southern corn rust fungus were filiform. The intercellular hyphae and intracellular hyphae had difference in monokaryon or dicaryon. The contact between the intercellular hyphae and the host cell induced the differentiation of haustorial mother cell. The haustoria appeared in the host cell after haustorial mother cell penetrating through the host cell wall. The host cytoplasmic membrane was invaginated in the place where the haustoria invaded into the host cell. The callus was generated to surround the haustoria neck with the development of haustoria. The urediospore had the numerous staggered spines on the surface. The rounded and recessed crista existed on the outside of the spines. The study offered the ultrastructural features and cytological features of infected institutions (haustoria) for southern corn rust fungus, and analyzed the nuclear phases among the different varieties and laid a foundation for the histopathology of southern corn rust fungus.