Gummy stem blight (GSB), a common and serious disease in cucurbits worldwide, is caused by three genetically distinct species: <i>Stagonosporopsis cucurbitacearum</i> (syn. <i>Didymella bryoniae</i>), <i>S. citrulli</i>, and <i>S. caricae</i>. In Korea, however, the three species of <i>Stagonosporopsis</i> have been barely characterized. In this study, 21 <i>Stagonosporopsis</i> isolates were recovered from watermelon (<i>Citrullus lanatus</i>) and muskmelon (<i>Cucumis melo</i>) leaves and stem showing blight symptoms collected from 43 fields in Korea. Sequence analysis performed with an internal transcribed spacer region was not competent to differentiate the <i>Stagonosporopsis</i> isolates. On the contrary, analysis of β-tubulin (<i>TUB</i>) genes and three microsatellite markers, Db01, Db05, and Db06, successfully differentiated <i>Stagonosporopsis</i> isolates. Further sequence analysis identified two <i>Stagonosporopsis</i> species, <i>S. citrulli</i> and <i>S. caricae</i>, and one previously unknown species of <i>Stagonosporopsis</i>. Representative isolates from three species caused dark water-soaked lesions on the detached watermelon and muskmelon leaves with no significant differences in the aggressiveness. Our results indicate that the <i>S. citrulli</i>, <i>S. caricae</i>, and unknown <i>Stagonosporopsis</i> sp. are all causal agents of GSB for both watermelon and muskmelon. This is the first report of a new species and the population structure of <i>Stagonosporopsis</i> species causing GSB in Korea.