Arbuscular mycorrhizal fungi (AMF) and dark septate endophytes (DSE) colonizing Panax notoginseng in three main producing areas in Wenshan Prefecture of Yunan province were investigated. The fungal colonization of 144 roots samples including healthy and rot roots of P. notoginseng with different age were observed by means of acid fuchsin stain. The results showed that P. notoginseng was the typical arbuscular mycorrhizal plant. Although there was no significant difference in AMF and DSE colonization among three sites, the total colonization of AMF was significantly higher than that of DSE. Statistical analysis demonstrated that the fresh weight of P. notoginseng root was positively significantly correlated with the colonization of AMF, but not with the colonization of DSE. These results suggest that AMF may play more important role than DSE in improving the yield and quality of P. notoginseng. Furthermore, AMF colonization of healthy P. notoginseng was higher than that of plant with root rot, which suggested that AMF could defend P. notoginseng against root rot pathogens. AMF have great potentiality and broad prospect to control root rot of P. notoginseng.