Stem rot symptoms were recently identified in greenhouse-cultivated paprika (Capsicum annuum L.) in Hwaseong, Korea, with the causal pathogen determined to be Rhizopus stolonifer. Diseased stem samples displaying water-soaked lesions and abundant black mold growth were collected for pathogen isolation. The fungus demonstrated rapid mycelial growth and typical sporangium formation on Potato Dextrose Agar (PDA), and its morphological characteristics were consistent with those of R. stolonifer. Temperature assays indicated optimal mycelial growth at 20–30℃. Artificial inoculation using a spore suspension (2 × 10⁶ spores/㎖) on pruning wounds replicated the characteristic soft rot symptoms and stem collapse within 10 days. The fungus was re-isolated from the affected tissues and confirmed again as R. stolonifer, thereby definitively establishing its pathogenicity and fulfilling Koch’s postulates. Molecular identification through 28S rDNA sequencing (668 bp) and phylogenetic analysis further supported the isolates as R. stolonifer. To our knowledge, this is the first report in Korea indicating that Rhizopus stolonifer, though commonly recognized as a postharvest pathogen, can also cause stem rot in greenhouse paprika via pruning wounds during cultivation. These findings emphasize the potential risk of disease spread under climate change and highlight the necessity for integrated management strategies throughout both cultivation and postharvest phases.