Ajwain (Trachyspermum ammi (L.) Sprague) is an important medicinal and spice crop widely cultivated in India. In recent years, its production has been affected by several fungal diseases, among which stem rot caused by Sclerotinia sclerotiorum (Lib.) de Bary has become a serious problem. A field survey carried out during the rabi seasons of 2022–23 and 2023–24 in the districts of Rohtas, Buxar and Nalanda in Southern part of Bihar revealed that the disease was widely prevalent, with incidence ranging from 39.03–61.89 %. Infected plants initially showed small water-soaked lesions on the stem which gradually enlarged and turned necrotic. As the disease progressed, abundant white cottony mycelial growth appeared on the affected tissues, along with the formation of sclerotia inside the stem. Severe infection often resulted in stem breakage and eventual death of the plant. The pathogen was isolated from diseased tissues and identified based on cultural and morphological characteristics, which were further supported by molecular analysis. On potato dextrose agar (PDA), the fungus grew a large quantity of white, fluffy mycelium, then colonies developed black, irregular sclerotia in concentric circles. Under the microscope, typical hyaline, branched hyphae (mycelium) of S. sclerotiorum were seen. Twenty ajwain germplasm lines were tested for resistance to the pathogen; none of the genotypes had complete resistance, but 2 lines (Rajendra Ajwain (RA)-14 and RA-16) showed moderate resistance. These lines may be considered for future breeding purposes.