Fusarium wilt, caused by Fusarium oxysporum f.sp. cubense (Foc), is one of the most destructive diseases of banana and has spread in many plantation areas in Indonesia. Until today, the effective ways to control banana fusarium wilt disease have not yet been found. Some studies indicated that Allium spp. could be used to suppress plant diseases caused by Fusarium. Allium spp. are important horticultural crops which are generally cultivated in some areas in Indonesia. This research was conducted to determine the effect of several species of Allium spp. intercropped with banana to improve soil suppressiveness against banana fusarium wilt disease. The results showed that up to 12 months after planting, from 3 species of Allium spp. (A. tuberosum/Chinese leek, A. fistulosum/bunching onion, and A. cepa var. aggregatum/shallot) intercropped with banana Ambon Kuning (AAA) cultivar, Chinese leek and shallot were able to suppress the incidence of fusarium wilt disease of banana by 46 and 33% respectively. Soil analysis on the rhizosphere of banana intercropped with Chinese leek and shallot had lower population of total Fusarium compared to the other treatments. Analysis of fluorescein diacetate (3'.6'-diacetylfluoerescein) or FDA also showed that total microbial activity in the rhizosphere of banana intercropped with Allium spp. was also lower compared to control treatment (without intercopping). The observation of the effect of Allium spp. extracts on Foc showed that Allium spp. extracts were able to suppress the development of the colony and spore germination of Foc in vitro.