Chinese chives (Allium tuberosum Roxb.) is an important allium crop in Korea. During winter of 2014-2015, typical symptoms of Sclerotinia stem rot were observed in commercial crops of Chinese chives ‘Green Belt’ in polyethylene tunnels in Iksan, Korea. Disease incidence ranged between 10 and 20%, causing considerable economic losses. Pure isolates made from symptomatic tissues were transferred onto potato dextrose agar (PDA) and consistently yielded abundant white mycelia developing sclerotia after two weeks. The pathogen was morphologically identified as Sclerotinia sclerotiorum (Lib.) de Bary. A voucher specimen was deposited with the Korea University Herbarium (KUS-F28606). A representative isolate was deposited with the Korean Agricultural Culture Collection (KACC47723). Genomic DNA was extracted from mycelia and the complete internal transcribed spacer (ITS) region of rDNA was amplified with the primers ITS1/ITS4 and sequenced. The resulting sequence of 558 bp was submitted to GenBank (Accession No. KJ614564). A BLASTn search revealed that the Korean isolate showed 100% identity with those of S. sclerotiorum (DQ329537, KF859932, KF859933, JN013184, etc.). Pathogenicity was confirmed by inoculating the lower stems of healthy Chinese chives ‘Green Belt’. Plants were kept in the greenhouse at 15 to 20°C and relative humidity > 90%. Symptom expression was evident after three days with Sclerotinia sclerotiorum consistently re-isolated from the symptomatic tissue, fulfilling Koch’s postulates. No symptoms were observed on control plants. This is the first report of Sclerotinia stem rot on Chinese chives globally as well as in Korea. Our field observations suggest that low temperature, high humidity, poor ventilation and continuous cropping cyles in non-heated plastic tunnels accelerate the incidence of Sclerotinia stem rot on Chinese chives. This crop is mostly grown with limited chemical control options; a Good Agricultural Practices (GAP) model for producing eco-friendly Chinese chives is currently under development.