Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai, Cucurbitaceae] is an important fruit crop in Taiwan. A severe foliar disease of watermelon cv. ‘China Baby’ with the disease incidence of 100% was observed in Chiayi city, Taiwan in 2017. Symptoms were circular dark brown necrotic spots and resembled symptoms of gummy stem blight. A fungus was consistently isolated from surface-sterilized leaf samples. After incubation on quarter-strength PDA for 14 days, the isolates, CL2 and CL3, formed dark olivaceous colonies with grayish aerial mycelia. The isolates did not sporulate under the experimental conditions. Based on the colony morphology, the isolates were similar to two morphologically indistinguishable but genetically distinct Stagonosporopsis species (Stewart et al. 2015), Stagonosporopsis cucurbitacearum (Fr.) Aveskamp, Gruyter & Verkley (Keinath et al. 1995) and Stagonosporopsis citrulli M.T. Brewer & J.E. Stewart (Stewart et al. 2015). The isolates were further identified by sequencing of the internal transcribed spacer (ITS) region of the rDNA and partial sequences of beta-tubulin (BTUB), chitin synthase (CHS), and calmodulin (CAL) genes (Stewart et al. 2015). The sequences were deposited in GenBank under accession numbers MG963959-MG963960 and MG968862-MG968867. The ITS sequences of the isolates showed 100% identity with Stagonosporopsis citrulli ex-type strain C5–5 (KJ855546) by BLASTn analysis. The CAL sequences of the isolates CL2 and CL3 were 100% and 99.8% identical to that of S. citrulli C5–5 (KJ855658). The CHS and BTUB sequences of the two isolates shared 100% identity with those of S. ctirulli C5–5 (KJ855714 and KJ855602). Multilocus sequence analysis of four concatenated loci (ITS, CHS, CAL, BTUB) of the isolates and reference sequences (Stewart et al. 2015) retrieved from GenBank was conducted. The two isolates clustered together with S. citrulli C5–5 in a well-supported clade, revealing that the watermelon isolates are S. citrulli. To fulfill Koch’s postulates, watermelon cv. ‘China Baby’ leaves were inoculated with the S. citrulli isolates according to the method of Rennberger et al. (2017). The inoculated leaves showed symptoms indistinguishable to those of natural infections. The same fungus was successfully re-isolated from the symptomatic leaves. The control leaves remained symptomless. Currently, the pathogen was recorded as causal agent of gummy stem blight on the same plant host in Georgia, USA (Stewart et al. 2015). To the best of our knowledge, this is the first report of S. citrulli causing gummy stem blight of watermelon in Taiwan.