Microorganisms are an extremely promising alternative to the extended use of pesticides for bio-control of plants. Pesticides are often expensive and accumulate in plants, having adverse effects on humans. Moreover, detection of undesirable chemical compounds in the food chain connected with the emergence of fungicide-resistant strains of pathogens calls for an alternative, non-polluting strategy for controlling plant diseases. Thus, biological control through the use of natural antagonistic microorganisms has emerged, for a long time; gram-negative bacteria have been intensively investigated as biological control agents. However, recently the attention has switched to the gram-positive members of the aerobic, spore-forming genus Bacillus. Bacillus amyloliquefaciens is an important Bacillus species because of its ability to produce different bioactive compounds with a broad spectrum of activity. The endeavor of this article is to review the literature on the utilization of bioactive compounds from Bacillus amyloliquefaciens in bio-control.