Soybean is one of the most important legume crops cultivated all over the world. Breeding of soybean plays a crucial role in developing new soybean varieties with improved traits, such as higher yield, as well as variety tolerance to pests, and shading stresses. This chapter discusses the key aspects of soybean breeding, including genetic breeding and molecular methods. Furthermore, the impact of intercropping soybean with maize in reducing the damage of soybean mosaic virus and other insects’ infestation was reviewed. The effect of cropping systems on gene expression as a potential strategy for disease control in soybean fields was also tackled. Genetic analysis of some Egyptian varieties of soybean for its tolerance to soybean mosaic virus and other insects’ infestation under intercropping was also provided.