Worldwide, researchers have identified soils that suppress soil-borne pathogens largely attributing this suppression towards the characters of antagonistic property or suppressive mechanisms for nearly 60 years. Now, the research has focused on understanding how native microbiomes can mitigate soil borne diseases even when pathogens, susceptible hosts, and favourable environmental conditions are continuously present instead of merely discovering and applying potential biocontrol agents in an inundate manner. Further, advances in next-generation sequencing (NGS) have now offered great deal of opportunities to re-examine and further explore the profile / characteristics of these suppressive soils. During the experiments, two broad types of suppression have been recognized: one is specific and other is general suppression, with corresponding theories developed around these concepts. This review highlights three current model systems that illustrate features of specific and general suppression related to suppression of take-all disease caused by Gaeumannomyces graminis var. tritici, Bare patch of wheat caused by Rhizoctonia solani AG-8, and interactions involving Streptomyces. To compare and contrast general versus specific suppression models, we propose several hypotheses regarding the nature and ecology of microbial populations, functions and composition in suppressive soils. In this chapter, we also discuss the potential and limitations of new molecular techniques for testing these hypotheses. Finally, we explore how a deeper understanding of the phytobiome can aid in the development of sustainable agricultural disease management strategies by leveraging the benefits of indigenous soil microbes by describing in following sub-heads.