Fusarium foetens is a new destructive pathogen on Begonia. This fungus is morphologically difficult to distinguish from other known Fusarium species. Moreover, the currently used assays for identification of this species require isolation and growth of the fungus which make the process time consuming. This study describes the development of a gel-based conventional polymerase chain reaction (PCR) test and a real-time PCR test for fast, practical, sensitive and specific detection of F. foetens. The gel-based PCR test presented amplifies a 275-bp fragment of the elongation factor (EF)-1¿ region. The real-time PCR test was based on the mitochondrial small subunit sequence of F. foetens. Both tests are suitable to detect F. foetens in cultures as well as in infected plant materials and offer potential for routine detection purposes.