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During seed health testing of 160 accessions of safflower, we observed some fungal growth on seed surface of four accessions i.e., IC337954, IC338197, EC182199 and EC181301 which were received from Hyderabad, Telangana, India for long‐term conservation in the National Genebank, ICAR‐National Bureau of Plant Genetic Resources, New Delhi, India. The associated fungus was morphologically identified as Diaporthe helianthi. Later on, the identity was confirmed as Diaporthe helianthi (Desm.) Grove by the sequencing of internal transcribed spacer (ITS) region (GenBank Id: KM979906.1). During seed health testing, seed infection of 30.0 to 70.0 per cent was recorded with no seed germination in infected seeds. Previous findings revealed that D. helianthi is host‐specific pathogen causing stem canker to sunflower only and the fungus is seed‐borne. As a destructive pathogen causing substantial yield losses, especially to sunflower, it may be a serious threat to safflower cultivation in the country and anywhere else. Therefore, the detection and identification of D. helianthi can be helpful in alarming the threat at an early stage thereby minimizing the probable damage to safflower cultivation in near future. [ABSTRACT FROM AUTHOR]