In order to discern commercial brewing yeast strains, a specific polymerase chain reaction (PCR) which targeted the open reading frame of AGA1, DAN4, HSP150 and SED1, was tested. Shochu yeast strains and wine yeast strains demonstrated that PCR products are highly polymorphic in length, and we could discern all of the test wine yeast strains and eight of the test shochu yeast strains. However, as PCR products of sake yeast are lowly polymorphic, we could not discern these except for K-11 individually. As the method based on the PCR to discern brewing yeast strains was simpler than classical physiological methods, it was useful to discern brewing yeast strains with these primers.