Fusarium basal rot (FBR) infecting shallot caused a significant yield loss to the shallot production. Severity of this disease was known to be highly diverse depending on the regions, varieties, cropping system applied and Fusarium species associated. This study was aimed to investigate the occurrence of Fusarium basal rot in several shallot cultivations in Bantul Regency. This study was carried out in five shallot fields representing midland (Imogiri Sub District) and lowland (Sanden and Kretek Sub Districts) of Bantul Regency. Survey of cropping system was performed in each field to identify the shallot varieties, intercropped as well as rotated crops. FBR occurrence were monitored in three different points per fields represented by 25 plants in each point. Our findings exhibited that cultural practice applied in shallot cultivation contributed more significant impact in decreasing the FBR occurrence compared to the geographical condition. FBR incidence varied among varieties and types of intercropping as well as rotation used. Among several aspects of cultural practice observed, application of intercropping and rotation suppressed the FBR infection significantly compared to the one cultivated in monocropping.