Since 2008, severe disease epidemics with symptoms resembling gummy stem blight have occurred on gherkin cucumbers (Cucumis sativus) in Karnataka, India. Three morphologically identical, but genetically distinct, Stagonosporopsis species, namely: Stagonosporopsis cucurbitacearum (syn. Didymella bryoniae), Stagonosporopsis citrulli, and Stagonosporopsis caricae, can cause gummy stem blight of cucurbits. Our objective was to use molecular techniques to identify if one or more of these species caused the recent epidemics on gherkin. It is not known which of these species is causing gummy stem blight of cucurbits in India. Based on the original host species, disease symptoms, fulfilment of Koch's postulates, and macroscopic and microscopic morphological analysis, the causal agent was tentatively identified as Stagonosporopsis sp. To identify which species was responsible, nine isolates were obtained from the outbreaks on gherkin in two regions of Karnataka in October and November 2014. The internal transcribed spacer region (ITS) of the ribosomal DNA was sequenced, and a previously developed PCR-based marker for distinguishing species causing gummy stem blight was used to identify the species of the isolates. We determined that seven of the isolates were S. caricae and two were S. citrulli. This is the first account in India that at least two Stagonosporopsis species are causing gummy stem blight of cucurbits, and are substantial threats to gherkin productivity and other cucurbits in India.