Root rot caused by Pythium spp. is a significant disease on greenhouse-grown crops and negatively affects the floriculture industry. To develop strategies that limit Pythium root rot on geranium and snapdragon, greenhouse trials were conducted to test plant protectants and cultivars. Seven fungicides and two biological control agents were evaluated on plants inoculated with P. aphanidermatum, P. irregulare, or P. ultimum. Disease severity was assessed using a scale of 1 (healthy, no disease symptoms) to 5 (plant death) from 5 to 45 day postinoculation (dpi). The area under disease progress curve (AUDPC) values differed significantly (P < 0.0001) among Pythium spp. and treatment. The interaction between plant protectants and Pythium spp. was also significant. For geranium, mefenoxam (trade name: Subdue Maxx) and Streptomyces lydicus WYEC108 (trade name: Actinovate) effectively controlled Pythium root rot. For snapdragon, treatment efficacy varied depending on the Pythium sp. When 11 geranium cultivars were inoculated with P. aphanidermatum, none were completely resistant to the pathogen. However, when P. irregulare was used to inoculate these geranium cultivars, Nano White Hybrid and Bulls Eye Cherry were similar to the uninoculated control. When 12 snapdragon cultivars were inoculated with P. aphanidermatum or P. irregulare, no cultivar was completely resistant to either pathogen, but Twinny White and Candy Showers Yellow were least susceptible to both. Integrating effective fungicides with less susceptible cultivars can limit disease caused by Pythium spp.