Samples of root rot disease of Medicago sativa were collected from Langfang of Heibei, Linhe of Inner Mongolia and Yanggao of Shanxi in 2013, to determine the dominant pathogens of alfalfa in these places. Pathogens were isolated from the samples and purified in PSA and MGA plate. Representative strains were selected based on biological characteristics,and then rDNA-ITS and TEF-1α sequences of the fungi were amplified and sequenced. Morphological and molecular biological methods were used for identification of the representative fungi, and then determined pathogenicity by back infestation test. We isolate 6 representative strains, named C1, C2, C3, C4, C5 and L1. The results showed that:C1 and C2 were identified to be F. tricinctum, C3, C4 and C5 were F. solani, L1 was F. proliferatum, which revealed that F. tricinctum was the main pathogens of alfalfa root rot in Langfang of Hebei province, F. tricinctum and F. solani were the dominant pathogens of this disease in Linhe of Inner Mongolia, and F. solani and F.tricinctum were the chief pathogens of Yanggao County of Shanxi province. The results of inoculation showed that L1 (DI 80.88%, DSI 61.35%) and C4 (DI 82.22%, DSI 59.6%) strains had higher pathogenicity, and C2 showed weakest pathogenicity (DI 54.44%, DSI 29.63%). There were no significant differences at disease incidence and disease severity index in C1, C3 and C5 strains, the disease incidence was 66.66%, 62.22% and 65.55% respectively; Disease severity index was 42.59%, 40.37% and 38.89%, respectively.