Bacillus subtilis strains isolated from different regions of Korea were screened for their plant growth promotion and induced systemic resistance (ISR) in tomato and red-pepper. The plant growth promotion on red-pepper and tomato revealed maximum plant height (22.73 cm) on red pepper treated with B. subtilis strain JE 21-1 and 30.18cm in case of tomato treated with B. subtilis strain JE 8-1. There was also significant improvement in root and shoot dry weight in both the plants. The strain JE 21-1 showed better promise for all growth parameters in red-pepper and tomato when compared to other strains and positive check BTH. Different strains screened in square plate method also revealed maximum plant height and leaf width, and suppressed anthracnose on red pepper in case of strain JE 21-1 at $10^6$ and $10^7$ cells/ml when compared to other strains. In all the bacterial inoculations the population was significantly high when compared to untreated check. In plant growth promotion with respect to fruit length and weight, fruit length was maximal in treating with JE 9-4 and ES 2-2, while fruit weight was maximal in treating with JE 3-6, ES4-2, ES2-2 and JE 21-2 on red pepper. In case of tomato, comparatively better fruit weight was in JE 21-1, ES 3-3 and JE 10-2 when compared to BTH and untreated control. The soft rot disease caused by Pectobacterium carotovorum SCCI was completely suppressed in case of transgenic tobacco harboring GUS gene related to PR1a and increased the level of salicylic acid significantly in combined application of JE 9-4 on par with BTH. Thus, this study clarified some potential Bacillus subtilis strains for plant growth promotion and ISR in red-pepper and tomato.