Bacillus subtilis Cot1 prevented Phytophthora and Pythium damping-off of Astilbe, Photinia, and Hemerocallis microplants and conventional Brassica seedlings under high-humidity conditions in fogging glasshouses. With Photinia, biocontrol activity was similar to that of the commercial fungicide metalaxyl when the antagonist concentration applied to roots was ≥3 × 105 CFU/g root fresh weight (RFW) and fungal inoculum was ≤102 oospores per g of peat. B. subtilis Cot1 colonized the developing root system of Photinia microplants and Brassica seedlings growing in peat substrate during the 28-day in vivo acclimatization period in the fogging glasshouse. With inocula of 4 × 106 and 3 × 105 CFU/g RFW, spore numbers remained between 105 and 106 CFU/g RFW in the older sections of the root system and between 104 and 105 CFU on root-tip sections. B. subtilis Cot1 application slightly reduced damping-off on Daphne plants. Poor persistence on Daphne roots and suppression of B. subtilis Cot1 by spent media of Daphne tissue cultures suggests that poor biocontrol activity was due to the release of inhibitory compounds by Daphne roots.