Rose flower is one of the most important cut flowers, with the world’s highest production rate. Soilless culture has been increasingly popular in plant production worldwide in the past few decades. In two separate trials, the efficacy of Trichoderma harzianum, Anearobacillus migululanas, slow filtration, and UV ultraviolet (UV) treatment and sand filtration in eliminating Fusarium oxyporum, artificially added in the recirculating nutrient solution, was evaluated with Rosea hybrid plants grown in closed soilless systems. The dynamics of these fungi in the recirculating nutrient solution and in the sand filter was also investigated. T. harzianum, A. migululanas, UV treatment and slow sand filtration were effective in reducing Fusarium root rot. However, slow sand filtration may be a more feasible disinfection method than UV because of lower costs of installation and maintenance and for its adaptability to a wide range of production systems. Moreover, these disinfection techniques can be successfully combined with the application of antagonistic microorganisms.