Fusarium crown rot of wheat has been spreading in the Huanghuai wheat‐growing area in China since 2010, leading to a potential yield loss. To investigate the pathogens associated with this disease in Jiangsu and Shandong provinces in recent years, 617 Fusarium isolates were isolated from nine sites in these two provinces between 2014 and 2016. Of these isolates, 372 were identified as Fusarium pseudograminearum, and the remaining isolates were identified as F. asiaticum and F. graminearum, suggesting that F. pseudograminearum is becoming a predominant causative pathogen of crown rot of wheat in eastern China. Trichothecene gene detection and chemical analyses of trichothecenes indicated that the F. pseudograminearum isolates belonged to the 3‐ADON or 15‐ADON chemotype, and one isolate had the NIV genotype but produced no detectable NIV. 3‐ADON isolates were predominant in Jiangsu, whereas 15‐ADON isolates were prevalent in Shandong. The mating type of the F. pseudograminearum isolates were identified. MAT‐1 and MAT‐2 existed, but in most collections, particularly those in Jiangsu, the ratios of the two mating types deviated significantly from an expected 1:1 ratio. The reason for the occurrence of F. pseudograminearum is hypothesized, and the chemotype and mating type distribution of this species in these two provinces are analysed.