This study was conducted to investigate the effect of grafting using commercial rootstocks and breeding lines on growth and resistance to both Phytophthora blight (Phytophthora capsici) and bacterial wilt (Ralstonia solanacearum), and to evaluate the breeding lines as candidates rootstocks for grafted peppers. Capsicum annuum ‘Nokkwang’ (scion) was grafted onto five commercial rootstocks (‘Kataguruma’, ‘Konesianhot’, ‘Koregon PR-380’, ‘PR-power’, and ‘Tantan’) and nine breeding lines (‘PR 901’, ‘PR 919’, ‘PR 920’, ‘PR 921’, ‘PR 922’, ‘PR 927’, ‘PR 928’, ‘PR 929’, and ‘PR 930’). Graft-take percentage was over 80% in all the grafted seedlings except those grafted onto ‘PR 901’ (75%). The number of leaves, stem diameter, leaf area, and dry weight of shoot of grafted seedlings were greater than those of non-grafted seedlings. Mineral contents in the shoots of grafted seedlings were significantly different, depending on rootstock genotypes. Marketable yield ranged from 1.35 to 1.96 kg per plant depending on rootstock genotypes, and was highest in peppers grafted onto ‘PR 901’ (1.95 kg) and non-grafted peppers (1.96 kg), and lowest in those grafted onto ‘PR 928’ (1.35 kg). Gross yield was highest in peppers grafted onto ‘Konesianhot’ (2.64 kg). Among nine breeding lines, three rootstocks (‘PR 920’, ‘PR 921’, and ‘PR 922’) were selected as candidate rootstocks for the grafted pepper based on graft-take, growth, yield, fruit quality, and resistance to diseases. Three major pepper cultivars (‘Nokkwang’, ‘Saengsaeng Matkkwari’, and ‘Shinhong’) were grafted onto those three breeding lines and ‘Tantan’ (control). Peppers grafted onto breeding lines of ‘PR 920’, ‘PR 921’, and ‘PR 922’ showed greater resistance to both Phytophthora blight and bacterial wilt without the decrease in yield and fruit quality. Accordingly, they were considered to be used as rootstocks resistant to both Phytophthora blight and bacterial wilt for pepper production.