Gram-positive bacteria, in particular, members of group Bacillus, are among the best-studied experimental systems in bacteriology. Research, in Bacillus subtilis is remarkably diverse, including genetics, biochemistry, cell biology, and ecology, thus has an enormous impact on both basic and applied biology. Multiple species of Bacillus and Paenibacillus occur in the agricultural fields that can promote the crop health in different ways. Some of these species directly stimulate plant growth either through enhancement in acquisition of nutrients or through stimulation of host plant’s defense mechanisms prior to infection; other species can inhibit or suppress the populations of pathogenic microorganisms and/or pests. Although the distribution, diversity, and population dynamics of these two genera have been widely studied using a variety of techniques, much remains to be learned if we are to improve both basic studies of plant–microbe interactions and bacterial ecology, as well as the efforts to improve agricultural technologies. Biological control, using microorganisms to suppress plant disease, offers a powerful alternative to the use of synthetic chemicals. Many species of Bacillus and related forms are potential biological control agents against various pathogenic microbes. Their spore forming ability makes them an ideal candidate for developing efficient biopesticide products from technological point of view. Many isolates of Bacillus spp. have been developed as biocontrol agents (BCAs) of plant pests and pathogens. However, a greater understanding of their ecology including diversity, distribution, and physiology of this Gram-positive genus will be helpful for identification of new strains to be used as successful BCAs. Development of molecular and genomic tools offers new possibilities for improving the selection, characterization, and management of biological control including modifications of wild-type strains to improve their ability for controlling soilborne diseases.