The contribution of crops and soil microbial community structure and functional diversity in soil-borne diseases control mulberry plant production is still inadequately understood. In this work, a comparative study was undertaken on the microbial abundance, community structure, and functional diversity in the soil rhizosphere between the resistant (Kangqing 10) and the susceptible (Guisang 12) mulberry genotypes. The study deployed the use of dilution plate method, micro-ecology technology, and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) techniques. The study aimed at developing better crop management methods for mulberry cultivation as well as preventing and controlling the occurrence and impacts of bacterial wilt on mulberry productivity. The results indicated that the soil rhizosphere microorganisms were more abundant in the normal resistant mulberry genotype than in the normal susceptible mulberry genotype. Carbon source utilization was better in the normal susceptible mulberry genotype. These properties were lower in the sickly resistant mulberry genotype than in the susceptible sickly mulberry genotype. Through the PCR-DGGE, it was shown that the bacterial and fungal community structures of the resistant genotypes were more stable than those of the susceptible genotypes. Through correlation regression analysis, it was shown that the mulberry bacterial wilt significantly contributes to the loss of soil nutrients, particularly organic matter and nitrogen, a possible cause to disrupted balance between the soil microbial community and the loss of soil organic matter. Resistant genotype plants displayed more resistance to bacterial wilt. Therefore, this study recommends the need to promote the cultivation of resistant genotype mulberry for increased yield.