Daylily (Hemerocallis citrina) is an important plant whose flowers are commonly used as a vegetable and in medicine in China. From June 2015 to July 2016, brown and rotted flowers, some of which were covered with white mycelia, were observed in a 0.8-acre commercial daylily field in Yanqing District, Beijing, China. Disease incidence was ∼40%. A total of 24 diseased flowers were collected. Based on cultural and morphological characteristics, molecular data (sequence analysis of the small subunit ribosomal RNA, elongation factor 1-α and β-tubulin regions) and pathogenicity tests, the causal agent was identified as F. proliferatum. This is thought to be the first report of F. proliferatum causing daylily flower rot worldwide.