In recent years, nanotechnology has attracted attention in many fields because it has several up-and-coming novel uses. Many researchers have suggested that chitosan nanoparticles (CS-NPs) and their derivatives are one of the best nanomaterials for delivering antibacterial activity. CS-NPs have a broad spectrum of antibacterial activity, but they manifest different inhibitory efficacy against gram-negative (G−) and gram-positive (G+) bacterial species. The mechanism of antibacterial action is an intricate process that varies between G− and G+ bacteria as a result of the differences in cell wall and cell membrane chemistry. In previous studies, greater antibacterial activity was more evident against G− bacteria than G+ bacteria, whereas in some studies G+ bacteria were more sensitive. Researchers predicted that the varied responses of bacteria are caused by the mixed hydrophilicity and negative charge distribution on the bacterial surface. Moreover, its activity depends on a number of variables including bacterial target (i.e., G− or G+ bacteria) and bacterial growth, as well as its concentration, pH, zeta-potential, molecular weight, and degree of acetylation. Therefore, this review examines current research on the mechanisms and factors affecting antibacterial activity, and application of CS-NPs specifically against animal and plant pathogenic bacteria.