Pteridophytes can establish stable symbiotic relationship with arbuscular mycorrhizal fungi (AMF), and significantly enhance their ability to obtain nutrients and resistance to environmental stress. To clarify the AMF colonization characteristics of different pteridophytes, a field survey and sampling of pteridophytes were conducted in Fengkai Heishiding Nature Reserve, Guangdong province. Furthermore, the microscopic and submicroscopic structures of pteridophytes-AMF symbionts were observed and analyzed by light microscope and transmission electron microscope, so as to illustrate the symbiosis characteristics between them. This study can provide valuable information for protecting and exploiting the resources of pteridophytes in South China. The results show that: (1) Hypha was the main infection form, but with the lowest infection rate of arbuscule among different pteridophytes. There were significant differences in the total AMF colonization rate among different pteridophytes. The top three highest colonization rate of AMF was Selaginella japonicum, Lepidopteris sclerotifolia and Pteris chinense, which was significantly higher than other species (P < 0.05). (2) Microstructures observation showed that hypha colonization was the main form of AMF colonization in the roots of all pteridophytes. Hypha could be found in the root cortex cells of all 9 pteridophytes, but not in the stele cells. (3) The hypha of AMF was composed by 2 to 3 layers of thin-walled cells with different thicknesses and shapes (i.e., oval and tabular). (4) AMF hypha and vesicles contained many vacuoles and lipids, which may be regarded as an important pathway for mycorrhiza to store energy. According to this study, we confirmed the widespread colonization of AMF in pteridophytes in terrestrial ecosystems. However, our study also found that the present forms of AMF in different root cells of pteridophytes were significantly different, probably due to plant physiological characteristics and interaction among habitat conditions.