Members of the Fusarium graminearum species complex are known to cause head blight of wheat. A natural nonpathogenic mutant, strain Fa0233007, was found in the strain collection of the Japanese F. graminearum species complex. In addition, this strain cannot form perithecia. Complete linkage of these deficiencies in the progenies obtained from crossing a wild‐type strain and the mutant strain suggested that a single genomic locus was responsible for deficiencies in both traits. The locus was mapped to chromosome 1 using sequence‐tagged markers. An NADPH oxidase gene (NoxA, FGSG00739) was identified in the mapped region, and a 2‐bp deletion that results in premature termination of the open reading frame was detected in the gene. Both pathogenicity and perithecium formation were recovered by FGSG00739 complementation in the mutant strain.