Daylily (Hemerocallis citrina) is a perennial herb cultivated in China and other Asian countries for its nutritional, medicinal, and ornamental values. During the growing season, leaf spot disease was observed on H. citrina plants in Yunzhou District, Datong City, Shanxi Province, China. Isolates JZ-DT1 and JZ-DT2, obtained from the diseased leaf tissues, were identified as Boeremia shanxiensis sp. nov. based on morphological characteristics and multi-gene (tub2, rpb2, ITS, and LSU) phylogenetic analyses. Pathogenicity tests demonstrated that these isolates could infect H. citrina leaves, inducing grayish spots with brown margins encircled by yellowish chlorotic halos via non-wound inoculation. This study is the first to identify and document B. shanxiensis as a novel fungal species and a new pathogen responsible for leaf spot disease on H. citrina. These findings provide crucial guidance for developing disease management strategies for H. citrina leaf spot.