Small amounts of contaminants may lead to false-positive results in sensitive polymerase chain reaction (PCR) detection systems. To analyze contaminants and understand the usability of β-glucanases in fungal preparations, we estimated the ribosomal DNA (rDNA) contamination in Zymolyase-100T and Lyticase by quantitative PCR. The amount of rDNA contamination determined by real-time PCR was 9210 copies/unit for Zymolyase-100T and 0.0323 copies/unit for Lyticase. The observations regarding these enzyme products indicate that careful consideration of contaminating DNA included in the reagents used for molecular diagnostics is necessary.