Natto, a Japanese soybean food fermented by Bacillus subtilis (natto), are often spoiled by bacteriophages. The contamination of natto by phages causes a rapid loss of viscosity of poly-γ-glutamic acid (PGA), which is a key factor affecting the quality of natto. B. subtilis (natto) phages were classified into 2 groups (I and II), based on the homology of their genomic DNA. A phage JNDMP (Group I) has a head (diameter, 60 nm) and a flexible tail (7 × 200 nm) and requires magnesium ions for propagation. JNDMP was found to be a generalized transducing phage. A virulent phage ONPA (Group II) has a head (diameter, 89 nm) and a contractile tail (9 × 200 nm) with a sheath (width, 23 nm) and requires no additional magnesium ions for propagation. The loss of PGA due to contamination of the phages is attributed to a PGA hydrolase, PghP, coded in the phage genome. The enzyme hydrolyzes PGA to oligomers via an endopeptidase-type action and rapidly reduces the PGA viscosity. These days, although contamination of natto with phages is relatively infrequent, phages still exist on the floors of factories. Controlling them via thorough cleaning of factories and hygiene education for workers seem to be the most important solutions.