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Aims:  Dwarf bunt of wheat, caused by Tilletia controversa Kühn, is a destructive disease on wheat as well as an important international quarantined disease in many countries. The objective of this investigation was to develop a diagnostic molecular marker generated from amplified fragment length polymorphism (AFLP) for rapid identification of T. controversa. Methods and Results:  A total of 30 primer combinations were tested by AFLP to detect DNA polymorphisms between T. controversa and related species. The primer combination E08/M02 generated a polymorphic pattern displaying a 451‐bp DNA fragment specific for T. controversa. The marker was converted into a sequence‐characterized amplified region (SCAR), and specific primers (SC‐0149/SC‐02415), designed for use in PCR detection assays, amplified a unique DNA fragment in all isolates of T. controversa, but not in the related pathogens. The detection limit with the primer set SC‐0149/SC‐02415 was 10 ng of DNA which could be obtained from 11 μg of teliospores in a 25‐μl PCR reaction. Conclusions:  An approach to distinguish T. controversa from similar pathogenic fungi has been developed based on the use of a SCAR marker. Significance and Impact of the Study:  Development of the simple, high throughput assay kit for the rapid diagnosis of dwarf bunt of wheat and detection of T. controversa is anticipated in further studies.

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