Fusarium crown rot of wheat has become more prevalent in China. To investigate the phylogenetic structure of Fusarium causing wheat crown rot in China, wheat basal stems with symptoms of the disease were collected from 2009 to 2013 in Jiangsu, Anhui, Henan, Hebei, and Shandong provinces. In total, 175 Fusarium isolates were collected and their mycotoxin chemotypes and distribution were identified. Among the 175 isolates, 123 were Fusarium asiaticum; 95 of these were the chemotype 3-acetyl-deoxynivalenol (3-AcDON) and 28 were nivalenol (NIV). Thirty-seven isolates belonged to F. graminearum, which were all 15-AcDON. Smaller numbers of isolates consisted of F. acuminatum, F. pseudograminearum, and F. avenaceum. The virulence of F. asiaticum and F. graminearum isolates on wheat crowns and heads was comparable. The virulence of isolates of the DON and NIV chemotype were statistically similar, but DON tended to be more aggressive. The DON concentrations in grains from wheat heads inoculated with isolates causing either Fusarium head blight or crown rot were similar. In the five provinces, F. asiaticum of the 3-AcDON chemotype was the predominant pathogen causing crown rot, followed by F. graminearum. Recent changes in causal Fusarium species, chemotypes, and distribution in China are discussed.