The search of food-grade proteases allowing broad application in food industry and protein modification is on increase worldwide due to pressure on the market of these enzymes as commodity product, both on price reduction and increasing performance. This paper reports nine protease-producing bacterial strains as new sources of food-grade protease from bacteria isolated from two Indonesian fungal fermented foods, soybean Tempe gembus and red oncom. Isolation was conducted on every other day within 5 days of storing (post fermentation) and protease production tests were then carried out on skim milk media agar. Cells of the isolated proteolytic strains were morphologically identified using SEM (Scanning Electron Microscope) and a bacterial phylogenetic tree was constructed using MEGA 7 program based on partial sequences of 16S rRNA genes of these bacteria. Based on taxa analysis and plate-based pathogenicity test, B. megaterium IROD3 and, B. amyloquefaciens IROD2, B. tequilensis ISTD3, and S. carnosus IROD4 appeared to be the potential candidates of food-grade proteolytic enzyme producers. This study concluded that prolonged fungal fermentation of soybean Tempe gembus and red oncom allowed growth of known low - nonpathogenic protease producing bacteria.