Introduction - Lisianthus ( Eustoma grandiflorum ) has become one of the major flowering plants in Okinawa, the southernmost prefecture of Japan. Simultaneously, many types of lisianthus diseases related to damping -off symptoms also increased dramatically. Objective and methods - To create a strategy for preventing the disease, disease symptoms and pathogenic organisms of primary problematic disease with seasonal variation in the emergence were investigated. Results and discussion - The symptoms were diagnosed as Fusarium root rot (Tachigare-byo) and the pathogens were identified as Fusarium nirenbergiae based on multigene sequences analyses. Indeed, our isolates, R2-28 and R2-29, are clustered separately from the other F. oxysporum strains isolated from lisianthus in Italy but R2-29 and the other F. nirenbergiae strain (MAFF 712464) isolated in Japan formed a monophyletic lineage. The diseased plants spread over the greenhouse from November to March. Furthermore, they increased to 2.3% of the total number in the case that no fungicide was sprayed, but there was almost no diseased lisianthus plant in the case that reductive disinfection of soil was conducted using ethanol, and fungicides were sprayed periodically after planting. Furthermore, the ratio of farms where Fusarium root rot occurred against the total number of farms was 56.3% in Okinawa Main Island. Conclusion - The pathogens of Fusarium root rot were identified as Fusarium nirenbergiae based on multigene sequences analyses. Reductive disinfestation of soil and spraying fungicides periodically within every two weeks was effective in preventing diseases, such as Fusarium root rot but not doing them in another greenhouse caused several Fusarium root rot.