The primary objective of this study was to determine the content of biogenic amines in Korean traditional fermented soybean pastes (doenjang) and to isolate potential probiotic Bacillus sp. with the ability to inhibit biogenic amines accumulation. There were significant differences in the bacterial cell counts, pH value, titratable acidity, salinity, and biogenic amine content between the samples. Among Bacillus strains isolated from doenjang, Bacillus (B.) licheniformis DB102, B. subtilis DB203, B. stearothermophilus DB206, Bacillus sp. DB209, Bacillus sp. DB310, B. coagulans DB311, B. cereus DB313, B. amyloliquefaciens DB714, Bacillus sp. DB917, B. cereus DB 915, B. subtilis DB1020, and Bacillus sp. DB1022 were found to be able to produce biogenic amines. On the other hand, biogenic amine-degrading strains were identified as Bacillus sp. DB403, Bacillus sp. DB407, B. subtilis DB517, B. licheniformis DB612, and B. subtilis DB821. In particular, Bacillus sp. DB407 and B. subtilis DB821 showed probiotic properties including tolerance to artificial digestive juices, adherence to intestinal epithelial cells, resistance to antibiotics, and antibacterial activity against biogenic amine-producing strains. In conclusion, the two probiotic Bacillus strains may be considered as the suitable starter for manufacture of fermented soybean foods with low biogenic amines content.