| Crown rot(CR) and Fusarium head blight(FHB) are two serious diseases in wheat caused by Fusarium pathogens. In order to screen new resistant sources and new resistant genes to CR and FHB, more than 1,000 wheat germplasms were collected from all over the world, of which 311 core germplasms were selected for identification and evaluation of resistance to CR at seedling and adult stage and to FHB. The resistance related sites to CR and FHB were identified by GWAS. The results showed that four germplasms including Cimrmanova, Jinan13, GHABAGHEB and Tumangmai had resistance to CR at both seedling and adult stages. Twelve germplasms including Longchun 8, Zhongmai 175, Lumai 5, Weimai 6, Wanmai 50, Reeves, Shijiazhuang 8, Xinong 928, Shanmai, SAFI-1/ZEM AMRA-1, Pingyan 181 and Shijiazhuang 54 were resistant to FHB. Five germplasms including Shanqianmai, Longchun 8, Neijiang 31, Liaomai 16 and Huaimai 22 had resistance to the two diseases. Especially, Longchun 8 was classified as resistant(R) to CR at adult stage and FHB, indicating that it is good resistance source for the two diseases. In addition, GWAS analysis showed that six SNPs on chromosomes 1A and 6B were significantly associated with resistance to CR-SR; 15 SNPs on chromosomes 1A, 1B, 3A, 3B, 6A, 6B and 6D were significantly associated with resistance to CR-APR; 13 SNPs on chromosomes 5A, 7A and 7B were significantly associated with resistance to FHB. This study provided useful information for utilization of CR-resistant and FHB-resistant wheat germplasms and laid a foundation for CR and FHB resistance in common wheat breeding.