Continuously cropping system of cash crops often destroyed soil microbial ecology with soilborn pathogens enriched but the number as well as species of beneficial strains decreased, leading to a shift from bacterial dominant type to fungi dominant one. Therefore, pathogens can more easily invade plant roots resulting in severe plant disease such as Fusarium wilt. Application of bio-organic fertilizers can reconstruct soil microbial community structure, consequently suppressing soilborne diseases. Advances on changes of microbial amount and diversity after continuously cropping and also the recovery tendency of soil microbial amount and diversity by applying bio-organic fertilizer were summarized. Furthermore, 454 pyrosequencing was introduced as a powerful tool by comparison with the traditional methods to analyze the microbial structure in the future.