Relationship between bacterial wilt of ginger with its soil biodiversity of freshly plowed soil, continuous cropping soil of ginger and continuous cropping soil receiving ecologically organic fertilizer (EOF) was studied by Random Amplification polymorphic DNA (RAPD) method. The results showed that ginger wilt did not occur in freshly plowed soil, while the ratio of ginger wilt was 100% in continuous cropping soil, and reduced to 37% when the continuous cropping soil receiving ecologically organic fertilizer. The soil microbial number of Fungi, Actinomyce is increased in continuous cropping soil receiving EOF, but a few changes of bacteria were found, as the varieties of strains in vitro were increased obviously. The simpson index, Shannon index all greatly increased after adding the EOF, which was similar to those in freshly plowed soil. The DNA sequence diversity of soil microbial communities was affected by EOF. The band of random amplification analysis showed a lot of amplification DNA bands in continuous cropping soil receiving EOF, and the distinctness that didn’t exist in continuous cropping soil emerged. The results of study suggest that applying EOF can enrich or decrease some microbial species in soil. It may also increase soil biodiversity and exhibit beneficial to suppress soil – borne pathogens on ecological level.